When I had the problem, it didn't occur during a red alert mission either. It was in the main FS2 campaign, Endgame I think.
I haven't looked into the problem any further so I don't know of a way to prevent the issue from occuring again, sorry. I don't know the root cause.
Did you switch campaigns with this pilot at all? The only interesting bit of information I got from my issue was that my pilot file had a blueplanet mission listed in the red-alert section, and I had been switching between blueplanet, blueplanet2 and FS2 to test if the Ant8 campaign switching worked correctly.
Would you be happy to open the pilot file in a hex editor? i.e. to look at what the corrupt data is?
EDIT: another idea - if you 7-zip the fie, how small does it get? If it compresses well you could upload it to mediafire or similiar for someone (me?
) to have a look at