I am wondering if there is a way to stop ATC from disconnecting me from an IFR plan if I am away. Sometimes I get up to get a coffee, and don't pause the game, and come back to find that ATC has been trying to get ahold of me since I left...

Is there a way to stop it from disconnecting, and maybe just go into a loop or somthing?

There is a way!  When the controller hands you off to the next controller, simply don't contact the next controller.  This will not effect your IFR flight plan.  You can do this for the whole flight, and when you are near the beginning of your descent contact whatever controller is now available.

DaveSims advice is the way to go. Canceling an IFR and requesting it again can be a problem because the ATC in FSX is a bit retarded, first they will turn you around back to your departure airfield, or send you 100nms out of the way, which can hurt you if you know how to manage fuel consumption. It seems that the controllers in FS9 must have went on strike and the controllers in FSX are 2nd rate replacements.