basically all existing Factory buildings now have a patch of ore inside of them after i ran the command to regenerate RSO Ores because i changed some settings and didn't want to start from scratch in a new world.
and one of my Factory buildings is completely missing all insides so it's just an inescapable black void (was probably caused by "CleanMap" mod, which deletes unused chunks).
crafting and placing new buildings shows none of these issues, so it only effected the already existing ones.

is there any way to repair existing buildings or do i have just make new ones?

You can use the Ore Eraser mod to erase the ore patches in your factory buildings, but there is currently no way to repair the CleanMap damage.

sad that buildings cannot be repaired, hope that gets added someday... somehow

there doesn't seem to be a 1.x compatible Ore Eraser mod right now so i guess i'll just have to live with them for now.