This has happened to me a couple of times with two similar (slightly complex) ships. I tried to create a save and then reload it, but while it calls itself "quicksave #1" that doesn't show up at all when I go to load a save. I also tried renaming it but with the same results. I had done some warping, but I've warped with other vehicles without a problem. When I loaded "persistent", it recovered the capsule with one Kerbal in it and the other two Kerbals were still in the lander, orbiting Minmus. They had the ∆ V to return to Kerbin and luckily as I had done this once already losing all my science (and two Kerbins I had to return to "Active" mode) I had put parachutes on it. I recovered them then and got all my science ... but this does not fix the issue.
**[EDIT]** Did 2 sub-orbital flights (one with transferring crew to the lander and back) no problem. Did another Minmus flight w/landing, on re-docking I could not go to the space center or tracking station. I could however revert the flight. Pretty sure it's the time warp (still).
**[EDIT 2]** Vanilla re-install, launched for Mun with a new ship with a separate lander. Used time-warp. Landed, launched, and when I went to re-dock I noticed that the RCS engines on the command module looked like they were blowing (same thing happened on the last ship now that I think of it, even though I removed all the RCS fuel from it). Docked, transferred crew, couldn't save or go to space/tracking centers. Reloaded from pre-Mun circularization, burned back to Kerbin, time-warped, landed, recovered everyone.
I think it's having a separate lander maybe? Damn, I hope not. (I did try landing the ships still docked, it was funny but it did not work, too top-heavy)
