Try this to see if it helps any (without doing
anything to your plugins):
1) Uninstall Sonar X3c (or X3b, if that's what you have).
2) Run a registry cleaner (carefully) to clean out ONLY the Sonar remnants, not that this step absolutely needs to be followed.
3) Install X3a (the first copy you downloaded to install). Don't open X3a.
4) Now, upgrade directly to X3c.
5) Open X3c, double-check your Prefs and scan for your plug-ins.
From what I've seen, all projects should retain your plug-ins, and those plug-ins should be just as good as they were in X3b.
I would also caution to double-check that (in Preferences) that you do not have "Replace VST2 with VST3" checked, if you're using any VST2's when migrating your projects. Waves plug-ins are OK to be swapped out automatically, since X3b's release.
A considerable amount of testing was done for Waves plug-ins, with CLSID issues, and crashes for X3c. I have no issues now with Waves plug-ins in X3c
unless I mix 32-bit with 64-bit, or VST2 with VST3's in the same FX Chain in ProChannel. I was one of the users more often able to have CLSID issues and crashes with Waves. Maybe this will help your projects survive the upgrade more seamlessly.
Lastly, IF this procedure helps, please let Cakewalk know. Maybe there is still an open issue moving directly from X3b to X3c that wasn't uncovered.