I thought you said any files you put in the userstore (correct, that is Drive E: or whatever else appears with the label "Kindle") have no effect and reappear after a while? Hence my suspicion it is broken somehow.
The "system" folder is inconsequential (it contains thumbnails of your books, various acx stuff, and other miscellany for the reader framework -- not the OS, that is in a hidden partition not exported to the computer -- but it will all be recreated as needed), but the tts folder will be lost. You may want to back that up if you plan on having your Kindle read to you with Text-to-speech. Also note that if kubrick actually starts working, it can replace missing tts files.
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