What causes Apple Music to delete my music files?

So I use mp3s, and recently, my hard drive got disconnected and I forgot to check where my files were saving to after I reconnected it. They were saving to my MacBook and not my hard drive. I caught that problem last night and moved all of my music files from my MacBook to my hard drive and reconnected everything to their files and whatnot. Well, then my genius wouldn't update and I couldn't get my I-Pod to load its library in Finder for me to sync it. So I restarted my MacBook, and when I brought Apple music back up, it essentially reset the entire library, and any mp3 that wasn't matched with a file in Apple Music's own library of music, is just completely gone. I also realized that any songs currently in my library since pulling it back up, I can't search them in finder. But when I go into my hard drive, all of my music is still there. So it appears that Apple Music has completely removed every single one of my mp3's and replaced every single one of them with a file from the apple store (at least the ones that they have a match for.) Why did it completely take all of my own music out of my library just for changing the location it's reading the files? I never had anything happen like this with iTunes, and it didn't do this to me whenever it started saving my files to the laptop and not my hard drive.

[Re-Titled by Moderator]

Original Title: Apple music library not acting correctly