Glad to hear you back up that folder. I helped someone recently restore ebooks from that folder in their backup records after a Reader Library reinstall wiped it clean, and they didn't know where their books went.
I misunderstood before when you said you back-up the Reader folder. I thought you were referring to folders on your ereader. When I plug in my 950 on my Mac, it shows up in Mac Finder (equivalent to Windows Explorer) as a drive icon titled "READER". I don't know if your ereader has a name or just a volume letter on your PC. My method is to back-up the annotations folder and cache files on the ereader. And, I also back-up my hard-drive folders too. Rather than keep copies of my ebooks in the kLibrary folder on my hard-drive, I keep all my ebooks in a specific folder on my hard-drive. That way they will still be there after a software reinstall.
The file path for kLibrary on a Mac is mostly similar. On a Mac, the path is:
Users/(username)/Library/Preferences/Sony Corporation/Reader/Database/kLibrary
When I went through my backup records, Markup wasn't a direct subfolder of kLibrary. There were several subfolders in between - can't remember the names. I also didn't have subfolders with book titles. I had two files in Markup. One was a jpg file, and one was a SVG file. They were for two different books. I don't move files over very frequently from my ereader to the hard-drive within Reader Library. I mostly use the collection sync feature to transfer files.
Currently I have no "markup" folder under kLibrary. I do have annotations on my ebooks that were imported into the Reader Library from copies on my hard-drive. So the annotations have to be stored somewhere... I think that perhaps you see annotations in your markup folder because of the drag-and-drop method that you use from the ereader to the hard-drive and the annotations you made on your ereader came along with the ebook file.
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