So when I upgraded to V10, I left all my V9 plugins on my system and didn't uninstall them. Which meant I had two copies of just about everything that got a V10 upgrade. Oddly enough this didn't seem to be a problem. Some hosts actually only showed one copy (SONAR/Bandlab and Cubase) but others like Reaper would show both, but they would both be usable.
Since Wave keeps saying you shouldn't have both V9 and V10 installed of any plugin I ran this utility. It seems to move the Wave plugins that are normally stored in c:\Program Files (x86)\Waves\Plug-Ins V9 and Plug-Ins V10 that you don't have licenses for to two new directories, Unused Plug-Ins V9 and Unused Plug-Ins V10. Just be sure to run it as admin.
Sadly this didn't fix Reaper from showing two copies. Only now the second copy wouldn't work. Had to do a full clear cache/re-scan, which was very painful. Between the iZotope plugins hanging because I use iLok authorization on them (a long running issue with their plugins) and the 10 minute+ timeouts that the Native Instruments plugins all take (due to the fact I've had/installed every version of NI plugins since the early 90's so my registry entry list is so huge they take forever to scan/load) it took a long while to get REAPER back. But once I finally got it through the scan (only a few crashes and a handful of restarts) my Waves plugins are now only listed once.
One of the threads on Gearsultz a Waves rep confirmed that once you get a V10 license all the V10 updates will be included even if your WUP expires. Just like it worked with V9. If they ever update any of the V10 plugins I have I'll be able to see for sure if that works, since my WUP has expired on a bunch of my V10 plugins recently.
With this utility I think the best upgrade for a mixed V9 and V10 world is. Update your licenses (on Waves website), install the new Waves Central, Install all the V10 plugins you have licenses for, don't take any of the V9 uninstall options during that process, then run this tool.