There is a limit to the number of files that can exist in a FAT32 directory. It is a rather strange limit, depending on both the number of files and the number of characters in the file names.
A synopsis of the details:
- There are 65536 entry slots available. A file takes at minimum 2 slots.
- The number of slots required equals floor((length of file name + 12)/13) + 1
This limit can lead to strange and seemingly unpredictable results. Deleting a single file with a long file name can allow storing of several file with shorter names. The site
https://blog.paddlefish.net/?page_id=1017 is a calculator of the number of files that can fit in a FAT32 directory, assuming an average length. The CC FAQ I referred to above has more detail.
FWIW: CC reports to calibre that all space is internal. Calibre cannot know if an SD card is being used. Reason: CC can control where book files are stored on a format-by-format basis.