I've been using RightClick for quite a while and really love it. However, I had the same problem as you, I think, the other day when upgrading to a new version (there have been a couple recently I believe). Other than this RightClick has been really solid most of the time that I have been using it. I've only had two instances where I lost anything.
Most recently, I lost all of the menu items that had sub-menus like Start Menu, Taskbar and System Tray and a couple others I had created manually. I'm not sure what happened or why, but I "think" it had something to do with one of the upgrades??? (just a guess)
In any case, I also just discovered recently that you can backup your RightClick menu by saving these two files:
C:\Program Files\Stardock\Object Desktop\RightClick\RightClick.ini
C:\Program Files\Stardock\Object Desktop\RightClick\desktopmenu.obbar
if RightClick is not installed in the same location as mine, you will need to make the appropriate adjustments.
I have been saving these files, but have not had the opportunity to do a restore yet because I have not lost anything since I found out about these files. But, it is my understanding that if you lose your RightClick menu, you can copy your backed up versions of these files back to the original locations, replacing the ones that are there, and everything should come back to what it was when you last backed them up.
I hope this helps....
-mike