Music Randomly Deleted

My wife just got a Strat 2 (her first smartphone). After loading up the SD card (a brand new one) with music, she popped it into her phone, and noticed only a fraction of her music was showing. I took the card out and investigated, and several of the folders had been emptied but not deleted. She had the songs organized into folders by genre (pop, dance, country, rock, etc...). Each folder contained a mix of formats (WMA, MP3 in various bitrates and codecs, OGG, and FLAC). I converted these all to MP3 files with LAME 3.98 @ 192kbps for the sake of uniformity, then moved them back, but some of the songs still won't play. I've verified these songs will play on a PC, so I know they aren't corrupted. The real kicker here is that, aside from the folders being emptied, there's neither rhyme nor reason to why tracks were deleted. If it helps, these were all one-deep folders in the root of the SD card.

I believe the default music player on the phone is Google Play Music, but I'm not 100% sure. If anyone can offer any guidance on why this would happen, I'd appreciate it immensely. She's getting tired of trying to work out while listening to George Strait, and I'm getting tired of hearing about it.