I had an existing directory with 8 iZotope plugins in:
C:\Program Files\VstPlugins\ (note the capitalization)
When I ran Waves Central v12.0.11 for the first time to install Waves SoundShifter v12.0.0, it seems to have overwritten that VST directory with another directory that uses different capitalization:
C:\Program Files\VSTPlugIns\
This new directory has no iZotope plugins and only the WaveShell2-VST 12.0_x64.dll file.
AFAIK Windows do not allow two identical folders with different capitalizations.
If I try to create a similar name folder using different capitalization, that new folder is not created rather ‘rejected’ by Windows.
In that sense, Central should be able to install to a folder with a different capitalization i.e.
C:\Program Files\ VstPlugins\ without deleting its content.
I suggest contacting Waves tech support regarding this issue.
I know a case exists on the Mac where you can “opt” to have a case sensitive drive format. However, I don’t know whether the same would be true for NTFS. I’d suspect so, I just have no experience of it.