I was really hoping to see a reply to this one, as I had a similar problem happen twice. In my case the keywords are still associated with the pictures, but my defined keywords revert to the original photoshop set.
I'm surprised that the keywords have disappeared from the pictures as they should be going into the XMP file for each individual picture and it is alot of work for a program gone bad to delete them all.
As for putting the keywords back into your definitions for Photoshop, I have a solution that works if the keywords are still part of your pictures. Select all your pictures (I do this folder by folder, but I'm fairly sure a search of all folders that put them all into the view would work as well), the keywords you have defined but that aren't part of your defined set will appear in italics. You can then right-click (at least on PC) and a menu come up that will let you put that keyword into the defined set.
If anyone knows how to save the file off so the defined keywords can be reloaded, I'd love to hear about it.
Joe