Ah - now that the forum is back open, I'll post the files I have about this bug. Attached is a copy of one of the projects I have that show it, its easy to reproduce.
Also, two screencasts based on that project. In the first one, I tried to add a cube shape to the end, and it recomputes everything, generating a lot of errors:
https://autode.sk/3JHe4cx
and a second one, where I try to add a cube thats not in connected to anything in the project, not even in the same component, and it also recomputes everything, with all the errors:
https://autode.sk/3iEzoTS
Now, I think this is showing two bugs:
1) doing the recompute for no good reason after a scale operation, which in a larger project gets annoying
2) generating lots of errors in the recompute. This is really more severe of a bug, since it shows that the timeline is not capturing all the data it needs along the way. A user should be able to traverse back and forth along the timeline at will, and it should work cleanly. Otherwise the timeline becomes useless, and it is such a powerful tool at the heart of the feature set! I never 'delete' a body, since it warns of these kinds of problems, but I do use 'remove' along the way to get rid of un-needed bodies, which should be okay.
In your earlier reply, you mention that the recompute seems to be a one-time thing - well, with all the errors, getting past that one time is a major issue! And deleting the history COULD get me past the problem, it means no going back and changing anything earlier in the timeline, a last-ditch option as you say, not a good thing.