[DNSB]

If you are storing your books in the root directory, you could fairly easily run into the maximum number of directory entries allowed (64K IIRC). Remember FAT32 stores the short file name in one directory entry and then stores the long file name in 13 byte chunks, each of which requires a directory entry. Running into the limit was why I now store my sideloaded ebooks in a directory in the root of the exposed storage. Shrinking file name lengths by using the :sublist(0,1,&) also helped (use the first entry in author_sort for the directory below ebooks and use title - first entry in author list for the filename).

In the Kobo driver configuration, I use "Ebooks/{author_sort:sublist(0,1,&)}/{title} - {authors:sublist(0,1,&)}"

If you are storing books in the root directory, I would suggest creating a directory and then sending your books there in blocks of 200 or so instead. If you back up your reading positions using Kobo utilities, you can restore them after the move.