Similar problem here.
I was working on my soundtrack for the Just Cause 3 Trailer using Sonar X3. Then I decided to take a look at the provided Sonar Demo. But when I continued to work in X3 a lot of instruments from the Sound Center were missing. So I removed the demo from my Steam library and ran a file check at the X3 Version, which reported 12k (or 1.2k, not sure right now) files missing. Right now, Steam is downloading 2.8 Gb ... I hope this will fix it for me.
Ok, the automatic file checking/redownloading via Steam did not help. But after I removed the corresponding DLCs from the Sound Center and reinstalled, the instruments are back now.