@mikeywilliams25: I am confused. According to the debug log you sent me, you did not attempt to connect. Assuming that you really did attempt to connect, the only way I see where nothing would be in the log file is if one of the extensions in the "Formats and folders" setting points to a non-existent folder in main memory. I will add this case to CC's logging.
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I did try to connect and then sent the log - I only have one setting for epubs which is pointing to the folder it wouldnt let me access for content or wifi connection. I've no idea why it didnt show up in the log.
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Having the private app folder work when other folders don't work also doesn't make much sense. By any chance are you running a non-standard Android system? Is your device rooted?
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Yes - I have TWRP installed. When i couldnt connect I read in your faq that one could change permissions if rooted - so I rooted but then found that permissions on the SD card could not be changed even with root.
I found this :
How to - Provide WRITE PERMISSION on sd card for apps on Android Marshmallow
1. Backup File - packages.xml in /data/system folder
2. Open File - in QuickEdit app
3. Search - for app name
4. Paste - <item name="android.permission.WRITE_MEDIA_STORAGE" granted="true" flags="0" /> in/after <perms> tag
5. Save - by pressing back twice and confirming Yes(Grant Root permission if asks)
6 Reboot - ur done.
I would try this but now that I have it working I'll leave it.
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If you are willing to take the time, what happens if you delete the former book folder "/books" then use CC to move the storage folder back?
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Sorry - it takes so long to copy my couple thousand books that I'm going to let sleeping dogs.....
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Regarding finding the books in the folder but not in the database, you can do that by connecting to calibre as a wireless device. CC will scan for books and try to match them with what is in calibre. This process is hit-and-miss because the metadata in the books can be wrong. You might find yourself needing to take the steps described in the FAQ
I have books calibre shows as "On Device" but not as "In Library". What do I do?. It is often easier to ensure that CC and calibre are in sync by deleting all the book files on the device (using a file manager) then resending them from calibre by connecting as a wireless device, searching for ondevice:true, selecting all, then sending the selected books to the device.