angstrom

Yes, that's exactly it (for me, anyway). In the aforementioned session, when I loaded a pre-1.13 craft it was missing parts as I described. As an experiment, I immediately loaded a new control module from the sidebar (the one I loaded with the craft did not seem to be acting as a root part) and once I did that, I was able to attach all the existing components to that part and all seemed well. Of course, you can imagine my hesitation with loading anything already flying! Again, once I reverted to 1.11, the saved craft loaded normally. Here's my gamedata dir: Good luck with finding the problem!

In the interests of helping you narrow down the problem (save game compatibility; ships are missing parts and connectivity, etc...) here's some more info: Last version I was using was 1.11. All was well. I went to 1.13 and the first ship I loaded in the VAB came up missing some payload parts and the entire boost section. The first thing I did was grab a procedural fairing that was just sitting there in its undeployed form and drag it to the sidebar upon which the game acted as if I had just thrown away the root part. I didn't risk loading anything flying. I backed out, reverted to 1.11 and as far as I can tell, everything is back to normal. To correlate with BigD145's mod set, I am not using LLL or Interstellar, but I am using SCANsat, although none of those parts were on the vehicle in question. I know that's a little thin, but maybe you can do a differential comparison on the last two point versions?