I had an issue similar to toric5 that seems to reproduce pretty well: 1. Launch craft, separate stages as normal 2. Dock to another craft once in orbit 3. Return to stages, land normally 4. Click 'Return to Main Mission' after landing last stage At this point I end up on the launch pad with another version of my pre-craft launch. The docked craft doesn't exist and what I docked to doesn't have it. I can recover everything for a profit, which isn't right I went through this many times and eventually figured out that if I dealt with the stages, then docked back on the main mission, everything would be fine.