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Personally, I would recommend creating a directory in the root of the exposed storage and copying your ebooks into that directory. The root directory of a FAT32 volume has a limited number of available directory entries and long file names chew them up rapidly.
A couple of other item is that you have .sqlite-shm and .sqlite-wal (SQLite shared memory and write ahead logging) files in your .kobo directory. Basically, those are an indication that the SQLite files were not properly closed before your Kobo was connected to the computer. If you connected from within KOReader, that indicates that the databases were not closed before you ran KOReader. If you are using the KoboTouch driver, this should trigger a database corruption message when you connect to calibre.
Secondly, your metadata.calibre file shows a file date of 2024-Sep-16 which suggests that calibre has not been used in months.
One advantage to using calibre is that you can clean up your metadata so you aren't guessing what the title and author names are for a file called 9b2742ca-30ec-43a1-b76e-68df27a65f82-epub-b68c8973-a363-4ec8-a82e-ae3f90346e85.epub
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