If bitters/players destroy some factory — remove its all entities and surfaces (for separate surfaces option), and for inner factories too (recursion).
It should free some CPU resources and make cleanup.

If it is laggy — add some button to shortcuts (for admins only) to process all killed factories for all forces for the whole map/surfaces.
Or make both:
1) shortcut button for admins
2) auto cleanup if some "Map" option is checked in settings (boolean) — we can start in auto mode, then switch to manual via admin button (megabases)

This feature is not needed

Factory buildings drop themselves on the ground if they are killed by biters/nuke/ect

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I expected the loss of the factory and internal content, and not to get another analogue of the immortal entity.
It's boring if you play with bitters.

The Problem, if you just remove dropped entities on the floor:
If I have a some power plant inside and some logic (combinators) with access to global surfaces (they sends commands — AAI Programatic Vehicles controllers) — they still send commands, and we do not have access to them.

In addition, if the internal content is resource-hungry enough (UPS), then if, after the destruction of the factory, I have to duplicate this content, it will consume UPS twice

it's all for option "Indestructible factory building" — off.