This happens over the years numerous times: If you upgrade Waves, so those waveshell.vst3s, Renoise somewhat starts to forget the new paths to the more recent versions of waveshell. This only if you disabled plugin scanning on Renoise start.
So on every reload of Renoise, you have to to do a scan of the plugins first, so then the path is updated again. After restarting, the path is again the old one.