I know this question is kinda ancient, But i just had the same problem with a buoyant offshore rig.
I flew it out there with jeb in the cockpit and a very low framerate, got in in place, then took jeb on EVA so i could recover him but leave the rig in place.
The instant i hit "recover" on jeb, my game crashed and i had to reload it.
It didn't seem like anything was wrong at first, i was able to ship a few kerbals out to it and it was fully controllable (though not sure if it was frozen in place because it's so heavy i wouldn't expect anything i did at the time to move it)
I realized there was a problem when i tried to launch a different mission and my game told me the rig was on the launchpad...
I am extremely reluctant to actually recover it because it was a monumental pain in the cheeks to get it out there in the first place.
Currently looking for ways to edit the .craft file to tell the game it's splashed down rather than at the launch pad, but if anyone already has a solution i, and i'm sure OP, would be extremely grateful.
