Fixed the contract mod issue. It turned out everything was being caused by the Lunkhod missions I originally edited, they're gone now. As for how they could have such an effect, I have no idea.
Just had a mission almost end in disaster, but managed to save it at the last second. The mission was the Soyuz-2 and 3 rendezvous. I had just brought the encounter distance down to 2km but failed to realize my perigee was now in the atmosphere. I was just barely skimming it with the lowest point reaching only 110km (the edge of the atmosphere is 130km with RSS) but with deadly reentry it was still very dangerous.
I was worried when a couple lights and some RCS ports blew up, but after I started gaining altitude again I was satisfied nothing important was going to burn up. I let my guard down and, while I wasn't paying attention, the spacecraft drifted and ended up with its side facing the wind. Before I could correct this the decoupler between the descent module and the service module exploded, leaving the craft adrift with no control or propulsion aside from the pod's inbuilt RCS.
I could have aborted the mission and waited for the orbit to decay, but there was one option left salvage it, risky though it may be. The aerobraking had actually improved my encounter and even with the lack of control at the end it was still under 500m. If the pilot could complete the encounter in EVA, she could take over the unmanned Soyuz-2. I figured it was worth a shot, even though the target was in a 250km circular orbit. She made it with barely any fuel to spare. She has one trial left: surviving reentry. My first Soyuz pod had deadly problems with aerodynamics once it got deep in the atmosphere. I attempted to fix it for this mission but it's untested. The danger isn't over yet.
Edit: My fix worked, and it was one of the smoothest reentries I've done. Never even got to 4g, Success!