Sorry for your loss. Never fun to put that much work and time into something and see it fail like that. Will try to reproduce this if possible. May be a super specific edge case.
Totally guessing here, but I have a theory:
The part that sticks out "might" be right on the line of a chunk. As you were flying back in, the chunk that contains the ledge ONLY loaded in first. The game then had a hang up in executing some other code, came back to the SI calculation, and then started an unfortunate chain reaction since the rest of the structure wasn't loaded in yet.
It would be interesting to take a look at your save file if you could upload it somewhere. You can PM me a link and I'll take a look.