I was using a 51xx version and when I ran the most recent svn version (5326) my save states were not compatable with it. Is there anyway to easly fix this? or.. will I have to load the 5100 version save to mem card, then load into 5326 and then make a new save state?
Nope, you have to do what you have to do;]. No other way.
Through what's soo important was added for you that you have to use newer one?;3 If you care only about some potential GSdx improvements, you can just copy new GSdx and use it with the older pcsx2 just fine keeping savestates(through after loading old savestate in different GS plugin I would recommend to press F9 twice to refresh any potential changes at least if you expect any;]).
Honestly no. Some changes break old states. I'd recommend, before updating, save to the memory card. You can still use save states, just be sure to save to the card every so often.