I know that several versions ago (pre-1.0) that there was a stability bug that would cause parts to start vibrating heavily on load, causing things to pull apart, explode, or some other nasty result. I've had a Minmus base for months now (that's real-world months) and haven't added anything to it in several days. I am running the KAS/KES mods, but again haven't done anything to this base for days, but unfortunately now, every time I switch to that base, or anything close to it, the ground starts violently shaking and all my stuff blows up and gets launched into the air. I know that clipping can be a part of this issue, but again that bug was supposed to have been fixed a while back. I can't find much info about this issue post-1.0, but I was curious if anyone had any ideas as to what I might be able to do to prevent this.
Here's a video of what is happening, as described above.
Update: I know that while in space (not in any atmosphere) you can stop rotation or otherwise shaky movement of spacecraft by quickly warping to the next warp level then back to 1x time. This culls the movement. I tried this on Minmus as soon as the base loaded, and it did stop the "quake". The problem is that as soon as I warped back to 1x time, it started all over again and the base still was destroyed. Not sure if that tidbit of info is useful to anyone.
Update 2: With the new 1.2 patch, I was hoping some of the stability fixes would resolve this issue, but either that's not the case, or the older version save game is not fixable. For now it will stay put on Minmus while I do other things, but I'm still looking for a resolution.
Update 3: In desperation, I loaded the base again, and it started to quake again after a few seconds. I went into warp x2 mode, and it stopped. Stayed there for several seconds, then went back to 1x, quake started again... I did this cycle about 4 or 5 times, and I noticed that the quake started more and more slowly (and with less intensity).. so I got the feeling that the few seconds before and after the time warp was allowing things to stabilize as the parts stopped moving. Another 10 or so cycles of this and I'm now able to sit in 1x (no warp) and have the base not explode. I was even able to turn off and retract my ore driller, and everything is still sitting here just fine.
So maybe that is the answer -- careful and precise timing of warp/unwarp to slowly calm the physics down. I'll wait a few in-game hours and see if it still works, then post it as an answer officially.