I hae same “issue” here as well.
I’m using VST2 version of Kontakt. I removed VST3 version from plugins folder because when opening older Cubase projects that have Kontakt vst2 in them, Cubase automatically loads Kontakt vst3 version instead of vst2, and all instances can’t find the patches for those tracks.
this is very strange because all other plugins both vst2 and vst3 version show up in Cubase and I can chose which one to use. But not Kontakt, if I put Kontakt vst3 in vst3 plugins folder then Cubase will only show Kontakt vst3 version and won’t be able to let me use Kontakt vst2.