Pekka Paalanen - 2016-05-15

Try not using /Music as the destination folder, but something you created yourself with unique name.

With Android 6 and Moto G 3rd gen, I had lots of trouble trying to copy my music into the /Music folder, it never completely succeeded, and Android also decided to randomly wipe the whole directory (no, not just making files invisible, the disk space was really freed) a few days after.

So, try using a folder name Android devs could not have guessed to make special. When I started using a folder name 'pq-files', everything worked fine with MTP and no files mysteriously disappeared.