When installing a new beta, I'm very cautious—I backup my installation, configuration and data, and then install the new version to a different directory. This time, since 0.9.9.9 is "released," I threw caution to the wind and installed it "on top" of 0.9.9.8. It worked flawlessly—as it should. All I had to do was disable a few plugins and scripts I don't use.
Just to be clear, I always backup my database and configuration prior to installing any new version. I prefer to backup the database by making a copy of it in Explorer, since this is faster and not dependent on the program for restoring it. Note the configuration file (pvdconf.ini) is saved the Windows "application data" directory.