Firstly, a bad ToC can only affect the device if the book gets opened. That might include when it is process after sideloaded. It might also include when the cover is generated to display on the home page or the library lists. If you restart the device and do your tests, the condition of the books will not come into it.
And something to try is to touch the screen after the disconnect. I sometimes see that my devices don't auto-sleep after disconnecting and unplugging from the PC. I don't have a real pattern, but I do feel that if I use it after the disconnect, it will sleep when I put it down.
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