I can't recall anything special about this save. This used no editor, no mods and no commands. I use some debug options from F4, but those are mostly visual (train length, path requests, pathing debug).
Maybe it was an upgrade issue? I played this save till the end for about two months after SA released and then returned to it about two months ago, so there was like 8 month gap. In particular, after restarting, the achievements were reset for some reason and then slowly filled up as I was playing, but it lead to some nonsense like this:

- obraz.png (227.77 KiB) Viewed 503 times
Maybe this game upgrade jump caused the concrete to glitch somehow?
I haven't really noticed anything special about Aquilo behavior after returning to it, I built most of it using blueprints or just by filling everything with refined concrete and then placing the heat pipes using blueprint containing heat pipe + normal concrete, so that it looks visually interesting.
For record, I play using standalone version downloaded from here directly, not steam release, so I doubt it could be caused by, for example, broken steam sync.
I occasionally play Biter Battles pvp mod (available in the
multiplayer list), it has its custom mods, but they sync on and off when I switch between multi and single player. It seem to restart the game completely, so I doubt it could be caused by this.