That's not good, indeed.
I suspect a compatibility issue with that USB drive. Which file system did you use when formatting? Personally, I've had success with ex fat, NTFS and FAT32, but maybe some combinations don't get along well.
I used NTFS, and the key is new.
I've tried with another one. A ssd one :
SanDisk Extreme Pro
1 - I put a folder with 293 files on it. And scan. It takes time but I wait less time than the 2000 files. Ok. The scan ok.
2 - I put a m3u playlist on the root. I try an experience, and I delet the 293 files. I load a folder of 40 files. -> After closed the WiiM Home app -" Opened it and Scan, nothing happened as the first USB key.
3 - I delet the wiim_cache (there was error, then I had to repair the key, before delet wiim_cache -as the first key aswell-) .
After it worst. The playlist is reconized, but WiiM Home scan 333 files on my USB key. Even if there is only 40 now.
Of course, I try to play the files I deleted, in WiiM home. Of course, nothing happens (Ultra goes ton the others one until it found the real 40 files).
The same trouble succeed with the first USB key. It's why I had to do a slow format with the first one, to rocover it.