I've had this issue too, but for my own music files. For me, it just does whole entire albums, that I am CERTAIN I had.
As proof of this, I have them on my iPhone 11, which required them to be in my iTunes library to begin with to make the transfer.
What's more, whenever I plug my iPhone in to then to copy the albums back from my iPhone (since they're still there), they just magically... don't show up when I am rooting around my iPhone's music library, using the Windows iTunes app, as does about 50% of the music files on my phone. This is unacceptable.
I have further banned iTunes from editing my Windows explorer file library, but it ignores these "preferences" that I set. Further still, it deletes the mp3 files from my Windows file library. Occasionally I catch them in my recycle bin in time, but not usually.
My workaround for this has been to copy all of my music files onto my D-drive, and then have iTunes playing the other files from my C-drive.
If anyone ever figures out a way to stop this from happening, I'm all ears.