"the format command ..." ??
What in the world are you even thinking about?
You will probably just make things worse.
That sounds like the indexer is having problems, see:
https://www.mobileread.com/forums/sho...d.php?t=237083
Since it is running continuously, keep it on external power, see same thread - about allowing the battery to fully discharge while it is running.
That can be death to its internal flash chip.
Try to keep it cool if possible - it will run faster and maybe fix itself sooner, see same thread.
It sounds to me like you need to use the 'do factory restore' using the USB flag file.
That will, among other things, reformat your USB visible user storeage.
Sorry, I don't recall its required spelling nor have a link handy.