Those 2 files are the log of what Calibre has
previously found ON THAT Drive. They are in the root of the drive regardless of where the books are.
The SD card is also a drive, so they should be there also
If they are missing, then Calibre has to rescan the whole drive(s) as the 'what is known'
shortcut is missing.
MTP is iffy in some cases. One thing: Only have 1 MTP device connected at a time.
This FAQ may help (a tiny bit)
https://manual.calibre-ebook.com/faq...or-kindle-fire