Well, To be exact I've had the 'flight3.dle' crash also happen when I've [alt]-[tabbed] out of LB2 and come back. That can happen even when I didn't fiddle with the flights on a re-fly. And to be fair, it has also crashed my game out-of-the-blue for no apparent reason. But 90% of the time if I get that crash and I didn't 'tab-away' from LB2 I am probably on a 're-fly' mission cause I did something stupid and don't want to give up yet.
A lot of times I will construct a mission around a set of objectives that are all close together. Like an insertion, a recon and say two different SAM/AAA strikes. I'll create a meet-up of all 8 helos and use the time-on-target and loiter times to get all the AI pilots to arrive and depart at the same time, and we'll all escort the insertion blackhawk or run CAP around one of the flights taking out an air defense site. It's even more insane if the Azer forces are flying crazy CAP missions in the area. I recently had a scenario where there were 6 enemy helos, and all 8 of my choppers flying around fighting each other...oh and I forgot to mention I called in in airstrike on the first set of Havocs, so there was an F15 circling the carnage!
I don't think I had ever heard so many stingers fired at once. Everyone was yelling 'Fox 2' and at one point I think a havoc took like 4 or 5 stinger hits as it was going down -- hilarious and awesome.
Now, when one spends that much effort constructing the mission and you realize an unknown ZSU-23 just over the hill is ahniliating your other flights, right after the meet-up, it's natural (if a little unfair) to want to adjust the mission on the 're-fly' to put in a SEAD objective to take it out, or to route the waypoints further away from the menace. Yeah it's cheating. But it's such a waste to throw all that hard work away. Back in Win98 days, I used to 're-fly' missions many many times -- sometimes as many as 11 times! Constantly modifying things on the re-fly to try and get my AI pilots to survive and increase their AI rating. I would get so pissed when on the 11th re-fly the 'flight3.dle' crash would wipe out my game and mission anyway.
It's one of the main reasons I stopped playing LB2 back then -- cause I would get so demoralized that all my AI pilots were always KIA. I could hardly ever win most of the mission objectives of my squad and it felt like Azer2000 was just too hard flying solo.