It appears that the mike force mission save is stored in your "YOURPROFILENAME.vars.armaprofile" file on the server. This is pretty standard for arma missions.
This means you can make backups of the .vars.armaprofile periodically and if you have your mission wipe, you can restore it.
I HIGHLY recommend doing this as it seems I am not the only person having the mission wipe after restarts. Something is corrupting the save and its starting a new one in its place. Until we get some kind of official response, I will be doing backups.