Check that missing plugin window very carefully... since both VST2 and VST3 versions of plugins have the same name. I had the same "wtf" when I opened a project in X2 created in X3... of course X2 couldn't find the VST3 plugins since they were introduced in X3.
Also, in Preferences->File->VST Settings, be sure the VST3 folder is in the scan path C:\Program Files\Common Files\VST3 is default, and also uncheck both of the VST3 Migration checkboxes (this allows SONAR to "see" both versions installed).
Just to be safe, I install both VST2 and VST3 versions of all plugins when available (you may have only re-installed one, and the project is using the other). You may need to re-install those again and select both versions.