Troubleshooting all manually transferred ebooks disappeared from my paperwhite

sovre · 10-20-2026, 05:46 AM

I use my kindle mostly offline and manually transfer most ebooks using calibre. It looks like the wifi got turned on and my kindle must have updated. Now the only books that show up on my device are Amazon kindle downloads. All the books I manually transferred from calibre are missing. It is also displaying a message that I need to register my device to access the cloud, which it never did before - but most of the books on my device were not in the cloud so that can’t be the issue. what has happened to all my manually transferred books and how do I access them?

What about all my notes and highlights and bookmarks? Is there any way to get them back?

I just connected my Kindle to my computer and looked in Calibre - when I click on show books on main memory of device, there is nothing there anymore. I'm assuming this measn I've lost everything?

I am just in absolute shock. This is not something that should happen on a commercial e-reader. Should you have to worry about your entire ebook library being wiped out in an instant because you turned on wifi? It shouldn't even be possible!

I obviously need to start to look at kindle alternatives.

shamanNS · 10-20-2026, 07:30 AM

That "bug" has existed for years and was discussed here:

https://www.mobileread.com/forums/sh...d.php?t=340936

Long story short: converted books that have cdeType "EBOK" and you didn't buy from Kindle Store will get removed after your Kindle spends enough time offline and then go back online.

For whatever reason Calibre still hasn't changed the defaults to create mobi and azw3 files that use cdeType "PDOC" to workaround that problem.
IIRC people here started using modified version of "Quality Check" plugin that had added option to set cdeType to "PDOC". And each time you convert new book with Calibre you would need to remember to use that plugin to edit the cdeType.

As for notes and highlights: do you still see "sdr" folders (folder with same name as book files + ".sdr" suffix at the end) in documents folder for all those removed books?
If content of sdr folders wasn't removed when the books themselves were you should at least be able to extract notes using this:

https://www.mobileread.com/forums/sh...d.php?t=322172

https://www.mobileread.com/forums/sh...d.php?t=375087

And if you kept those book in Calibre library in Kindle format ( if it doesn't neet to re-convert the book from epub or whatever before sending it to Kindle) resending the books would probably be able to still reuse files in sdr/ "sidecar" folders that stores the notes and highlights. As long as it's the same file with same GUID and ASIN values.

sovre · 10-20-2026, 07:51 AM

Thanks for your detailed explanation.

I looked in the directory of the device after connecting it to my computer and unfortunately the folders are empty. Nothing left in the documents folder. No text clippings file, no empty book folders, nothing. From the look of it you would think the device had simply decided to format itself.

Just unbelievable. I’m speechless. Can’t even process it.

shamanNS · 10-20-2026, 08:29 AM

Maybe Calibre "cleaned up" "orphaned" sdr directories? When you switched it to device view

IIRC when you use Calibre to delete the books it also removes the "sidecar" files.

If you really really need the notes & stuff you could maybe try using some of those "undelete files" type of programs like Recuva (if that even can scan removable drives

) to scan Kindle removable drive and see what can be restored (just make sure to use partition on you computer as an output directly, not Kindle itself).

sovre · Yesterday, 03:02 PM

Shaman, I wanted to update you on the situation, and I'm hoping you might be able to give me a bit more guidance, as you have a lot of technical knowledge about how the Kindle works which I lack.

First I wanted to tell you that I figured out what happened. Last year I had some of my accounts get hacked and I changed my Amazon email address at that time. My Kindle has been offline that entire time so it wasn't an issue. But it got accidentally connected to wifi just recently, and it seems what happened is that because my Kindle is registered to an email address that no longer matches my current Amazon email address, the software decided to wipe the entire device. That is why I lost all the document folders as well as my clippings. Everything was erased. And that is why my Kindle was asking me to register on restart.

I took your advice and used some recovery software to try and recover the contents of my Kindle. Altough most of the folder names themselves have been lost and the folders are designated by names like DIR641 and DIR642 it looks like the recovery software was able to restore most of my sideloaded books, as well as the SDR files that you mentioned. That is the good news.

But there is one big problem: before I recovered the files, when I was trying to figure out what happened to my device after it was erased, I had installed one ebook on my device, and I began reading that book and using the highlight function while reading. Because of this my device has created a new "my clippings" file for that one book. And apparently as a result of this the recovery software cannot find the original, much larger "my clippings" file which is actually the most important file to me, because it contains years of my own personal reading notes. Do you think my original "my clippings" file is lost forever because it was overwritten with a file of the same name, or is there some way I can get it back? I have no idea how to find it.

Do I understand correctly from what you wrote that the SDR files also contain the information that is saved in the my clippings file? or do they just have information about reading position?

I'm trying to figure out what my next step should be. I'm looking at the links you sent me about ways to extract notes from SDR files in your first post, but I'm very confused about how to make use of the information in those posts you linked to, as it seems very technical and all of this is new to me.

My priority for recovery is my personal notes in the lost "my clippings" file, and after that my highlighted passages, and after that my bookmarks.

j.p.s · Yesterday, 05:58 PM

The clippings file is just a log file showing that notes, highlights and bookmarks got made. The kindle never reads it, only writes.

kindle-reading-dashboard
https://www.mobileread.com/forums/sh...d.php?t=373997
reads information from the files in the .sdr directories and presents them in an organized manner.

You should be able to open yours books and navigate to your notes, highlights and bookmarks. If you can't, then they have lost connection to each other because of having different names or being in different directories.

Did you undelete the .sdr directories and their contained files? If not, when you undeleted the books, the kindle created new .sdr directories, which will not have your notes, highlights and bookmarks.

10-20-2026, 05:46 AM	#1
sovre Zealot Posts: 119 Karma: 10 Join Date: Dec 2010 Location: United States Device: iPad Mini; iPhone; Kindle Paperwhite (10th gen)	all manually transferred ebooks disappeared from my paperwhite I use my kindle mostly offline and manually transfer most ebooks using calibre. It looks like the wifi got turned on and my kindle must have updated. Now the only books that show up on my device are Amazon kindle downloads. All the books I manually transferred from calibre are missing. It is also displaying a message that I need to register my device to access the cloud, which it never did before - but most of the books on my device were not in the cloud so that can’t be the issue. what has happened to all my manually transferred books and how do I access them? What about all my notes and highlights and bookmarks? Is there any way to get them back? I just connected my Kindle to my computer and looked in Calibre - when I click on show books on main memory of device, there is nothing there anymore. I'm assuming this measn I've lost everything? I am just in absolute shock. This is not something that should happen on a commercial e-reader. Should you have to worry about your entire ebook library being wiped out in an instant because you turned on wifi? It shouldn't even be possible! I obviously need to start to look at kindle alternatives. Last edited by sovre; 10-20-2026 at 05:52 AM.

10-20-2026, 07:30 AM	#2
shamanNS Wizard Posts: 1,214 Karma: 12360292 Join Date: Feb 2010 Location: Serbia Device: Kindle PW5, Kobo Libra 2, Kindle PW1	That "bug" has existed for years and was discussed here: https://www.mobileread.com/forums/sh...d.php?t=340936 Long story short: converted books that have cdeType "EBOK" and you didn't buy from Kindle Store will get removed after your Kindle spends enough time offline and then go back online. For whatever reason Calibre still hasn't changed the defaults to create mobi and azw3 files that use cdeType "PDOC" to workaround that problem. IIRC people here started using modified version of "Quality Check" plugin that had added option to set cdeType to "PDOC". And each time you convert new book with Calibre you would need to remember to use that plugin to edit the cdeType. As for notes and highlights: do you still see "sdr" folders (folder with same name as book files + ".sdr" suffix at the end) in documents folder for all those removed books? If content of sdr folders wasn't removed when the books themselves were you should at least be able to extract notes using this: https://www.mobileread.com/forums/sh...d.php?t=322172 https://www.mobileread.com/forums/sh...d.php?t=375087 And if you kept those book in Calibre library in Kindle format ( if it doesn't neet to re-convert the book from epub or whatever before sending it to Kindle) resending the books would probably be able to still reuse files in sdr/ "sidecar" folders that stores the notes and highlights. As long as it's the same file with same GUID and ASIN values. Last edited by shamanNS; 10-20-2026 at 07:35 AM.

Yesterday, 03:02 PM	#5
sovre Zealot Posts: 119 Karma: 10 Join Date: Dec 2010 Location: United States Device: iPad Mini; iPhone; Kindle Paperwhite (10th gen)	Shaman, I wanted to update you on the situation, and I'm hoping you might be able to give me a bit more guidance, as you have a lot of technical knowledge about how the Kindle works which I lack. First I wanted to tell you that I figured out what happened. Last year I had some of my accounts get hacked and I changed my Amazon email address at that time. My Kindle has been offline that entire time so it wasn't an issue. But it got accidentally connected to wifi just recently, and it seems what happened is that because my Kindle is registered to an email address that no longer matches my current Amazon email address, the software decided to wipe the entire device. That is why I lost all the document folders as well as my clippings. Everything was erased. And that is why my Kindle was asking me to register on restart. I took your advice and used some recovery software to try and recover the contents of my Kindle. Altough most of the folder names themselves have been lost and the folders are designated by names like DIR641 and DIR642 it looks like the recovery software was able to restore most of my sideloaded books, as well as the SDR files that you mentioned. That is the good news. But there is one big problem: before I recovered the files, when I was trying to figure out what happened to my device after it was erased, I had installed one ebook on my device, and I began reading that book and using the highlight function while reading. Because of this my device has created a new "my clippings" file for that one book. And apparently as a result of this the recovery software cannot find the original, much larger "my clippings" file which is actually the most important file to me, because it contains years of my own personal reading notes. Do you think my original "my clippings" file is lost forever because it was overwritten with a file of the same name, or is there some way I can get it back? I have no idea how to find it. Do I understand correctly from what you wrote that the SDR files also contain the information that is saved in the my clippings file? or do they just have information about reading position? I'm trying to figure out what my next step should be. I'm looking at the links you sent me about ways to extract notes from SDR files in your first post, but I'm very confused about how to make use of the information in those posts you linked to, as it seems very technical and all of this is new to me. My priority for recovery is my personal notes in the lost "my clippings" file, and after that my highlighted passages, and after that my bookmarks. Last edited by sovre; Yesterday at 03:15 PM.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
All the books transferred from Calibre have disappeared on my Kindle !	Dalva88	Amazon Kindle	6	06-29-2023 01:21 PM
All the books transferred from Calibre have disappeared on my Kindle !	Dalva88	Calibre	5	06-25-2023 07:21 PM
library books have to be deleted manually on paperwhite	willaful	Amazon Kindle	5	10-07-2022 09:24 PM
Question: Manually sideloading onto a Paperwhite	haertig	Amazon Kindle	4	10-19-2020 02:55 PM

10-20-2026, 07:51 AM	#3
sovre Zealot Posts: 119 Karma: 10 Join Date: Dec 2010 Location: United States Device: iPad Mini; iPhone; Kindle Paperwhite (10th gen)	Thanks for your detailed explanation. I looked in the directory of the device after connecting it to my computer and unfortunately the folders are empty. Nothing left in the documents folder. No text clippings file, no empty book folders, nothing. From the look of it you would think the device had simply decided to format itself. Just unbelievable. I’m speechless. Can’t even process it.

10-20-2026, 08:29 AM	#4
shamanNS Wizard Posts: 1,214 Karma: 12360292 Join Date: Feb 2010 Location: Serbia Device: Kindle PW5, Kobo Libra 2, Kindle PW1	Maybe Calibre "cleaned up" "orphaned" sdr directories? When you switched it to device view IIRC when you use Calibre to delete the books it also removes the "sidecar" files. If you really really need the notes & stuff you could maybe try using some of those "undelete files" type of programs like Recuva (if that even can scan removable drives ) to scan Kindle removable drive and see what can be restored (just make sure to use partition on you computer as an output directly, not Kindle itself).

Yesterday, 05:58 PM	#6
j.p.s Grand Sorcerer Posts: 6,117 Karma: 107552269 Join Date: Apr 2011 Device: pb360	The clippings file is just a log file showing that notes, highlights and bookmarks got made. The kindle never reads it, only writes. kindle-reading-dashboard https://www.mobileread.com/forums/sh...d.php?t=373997 reads information from the files in the .sdr directories and presents them in an organized manner. You should be able to open yours books and navigate to your notes, highlights and bookmarks. If you can't, then they have lost connection to each other because of having different names or being in different directories. Did you undelete the .sdr directories and their contained files? If not, when you undeleted the books, the kindle created new .sdr directories, which will not have your notes, highlights and bookmarks.