It shouldn’t really matter what shell you are running as everything Waves should be backwards compatible. It should work as long as you have identical plugins.
So perhaps the problem is FL Studio. I now its been experiencing quite few issues lately, largely because of the Visual C Redistributable file issue. Not really a Mac issue to my understanding.
It might be a problem with the plugin cache if FL Studio uses one. You could try deleting that. You could also try uninstalling and reinstalling the Waves plugins too, if you haven’t already.
My problem was that Studio One couldn’t find WaveShell1-InternalSynth-VST 12.7_x64.dll, so when I tried to open a vst presumably associated with this waveshell, I got the black gui and the error msg that there was a problem with the wave shell. I searched for the location of the wave shell on my computer and relocated to common files/VST3. Studio One was able to find (or more like read/see) the wave shell and now the plugins work. Certain file types apparently can only be read in certain folders. In this case, I put it in with the other .dlls.
I’ve found with the Waves ecosystem that its better to leave their elements where they lie as moving them tends to break any dependency links they have.
It sounds to me, though I’m no expert at this, that somehow the WavesShell1 got moved about or placed into the wrong location. If that is the case it would certainly go along way to explain why things weren’t working for you and why placing it back gets it working again.