A couple times during my current play, I have been tracing empty belts only to discover the factory building that was making that thing is still on the map but is now mysteriously empty. Where it used to be filled with buildings and belts, it is now an empty factory building. When this has happened, the overlay icons have also been cleared.
The first time it happened I thought i must have accidentally deleted the interior. But the second time it happened, two different factories simultaneously became empty on the same map.
/give-lost-factory-buildings did NOT return the factories in question (but did return a bunch of others).
I have before and after saves available, with the factories present but populated in the first save, then present and empty in the second save, if that is useful to you for debugging purposes.
Other info:
* I have many mods installed including K2/SE, AAI industries, miniloader, advanced fluids, LTN, and a ton of QoL mods. I am happy to provide a full list if that's useful.
Thanks much!
BTW, this is my first game with this mod and I must say I absolutely love it. If Factorio is like coding, Factorissimo allows for clean & modularized code. It's the best!!