I sync my phone, I saw all the music on the list.
A few seconds later, a message said deleting.
I saw list of song after song being deleted.
When it's sync, it used a folder in folder hierarchy, I normally use Artist - Song.
I noticed that some folders were no longer on the phone, re-adding the Music directory did not re-add the songs.
When I copied it manually and noticed that the 200 songs are gone, this one at least did not delete the files.
I had to re-add the folder which is annoying but at least the files are still there.
I was traveling while the first issue happened so it was a bad scenario for me.
It was not another app since it was in MM who was displaying the deletion.