So, I decided to do a little house cleaning on my work machine and remove the beta version of the new FF browser (Minefield). And true to it's name that's exactly what happened when I tried to remove it. It asked me if I wanted to remove personal files associated with the Minefield app and I stupidly said yes. Then when I opened my normal Firefox, everything was gone.
Thankfully, it didn't take too long to get the plugins reinstalled and my bookmarking is all done with Delicious these days so it wasn't a complete hassle but it was slightly inconvenient.
I think it was actually good to do though cause my FF was starting to take a little bit long to start up due to excessive plugins I think.