I might worry too much but since they are not indestructible, wouldn't random biter spawns rid some of those? We can't craft them and they're such a big deal here, i wouldn't want to have a chance of losing any of them.

Buildings have an extremely high health pool, and if they are made invulnerable, the only way to demolish them will be lost

I could imagine setting their physical and acid resistances to 100%. Player could still kill them with grenades or flamethrowers. That still doesn't fix it for modded enemies that might explode on contact for example.

I tried making changes to the mod but it seems destructible-property is removed from the game some point, and there is no way to do it now that i can see. I have no intention of moving any of the factories, that is their point to be a foundation for the rail world. Losing one would be really bad, i use very high frequency enemy settings in my world i'd like to have more than 1 still alive in the world before i get there to defend.

Invulnerability is applied during the final stage of the mod—we simply take all registered damage types and set their resistance to 100 (except for repair)

I found the resistances code in proto-utils.lua, i had missed that. They're at 99% resistance but maybe that works for me... I heard from discord that setting entity.destructible = false only works in runtime. So maybe only when one is placed in a world, it just didn't work when i tried it in data phase. Can confirm it's found in API. Could still be a mod option if someone wants absolutely peace of mind about the topic xD

Okay, I think in the next update I'll add an setting to mark buildings as indestructible.