If you're flying on an IFR flightplan, and you fail to reply to ATC instructions, ATC services will be cancelled
When that happens (it happened to me today on my (non complete) transatlantic flight) what you do is you open your In FLight Planner and just open the same one you started with, but, click NO when it asks you if you want your aircraft to be placed at departing AP.
You don`t need to go that far. All you do is contact the nearest airport and ask for an IFR flight once again, no need to replan, even if the same plan. It often happens, when I go to make a brew and don`t pause, the flight crew just take too long to fetch one, got to do it yourself.....
It does sound though that the original poster has more problems than that. Maybe a clean install is called for.....
Reider