Is there a way to protect mesh from rebuild?

I ctr-q, ctr-s out of habit every few minutes – a life saver when modeling, protecting model changes from being lost to SW crashes. When working in simulation though it's the exact opposite problem; one ctr-q, ctr-s later and results that took all night to run are rendered unavailable – please re-run your six hour long study... Can simulation really be this temperamental?