It sounds crazy, but it is true. Apple is deleting music from subscriber's computers...on purpose. When you sign up, Itunes evaluates your music library looking for matches. When it finds what it considers a match, it deletes yours. After all, you can stream it from Apple Music now. Until you stop paying. Or don't have access to the internet.
When it finds music that's not matched in Apple's library, (like an original composition) it uploads the music, sometimes reducing the quality, then deletes the file from your hard drive. Don't worry, you can just continue to stream it from Apple as long as you have an internet connection and you keep paying them.
If this has happened to you, you'll want to first cancel your Apple Music subscription. Make sure icloud isn't set to backup music files. Then, restore a backup. If you need help navigating this issue or implementing automated backups, contact us here.