Apple confirms Apple Music is deleting some files - fix on the way
Apple itself hasn't had anything to say on the matter up to now but the tech giant is finally admitting that there might be an issue with the way the software is working.
A statement to iMore reads:
At the moment, iTunes works to scan your files and will sync them to the cloud and, in some cases, delete the originals. That's obviously not a great way to operate, especially when dealing with musicians who don't want their own material available to Apple's servers.
It's a bit of a concern that Apple can't replicate the issue themselves, which might make a proper fix difficult to pull off. We'll have more news soon.

