I've had this issue several times. Unfortunately I was not able to resolve this, though I've tried many different things:
- Re-uploading the files again, moving across different folders
- Rebooting kindle
- Checking file permissions and collection views etc.
The only thing, that worked for me, unforturnately, was to do hard-reset, and then upload everything again... (of course firstly I've put copied everything to some backup folder on my PC).
One issue with doing that was that some books even lost progress tracking... and after further analysis it looked to me like there was some format change, e.g. progress files (I think those are files with *.mbs extension) had some hashes (some random set of characters) in their name, which I had to delete and then suddenly progress was visible, etc.
It got me thinking some time later, whether there was maybe some updates along the way, but I did not confirm that...
Anyway - blunt answer for me was: swear a alot, then calm down and backup everything, do hard-reset, upload it back and try to still love your kindle.
Edit: I just found a method that worked for me, move the "books" folder to a different location, restart the books app, maybe restart the kindle, eventually, all the old books will go away from the app's library. Then move the "books" folder back to where it belongs. I restarted the app and the kindle again and read a kindle store book for a while and when I went back to the library, all the mobis were there in the library.