must be some mod that destroys entities on the mined event, so the event doesn't fire for other mods anymore.
i'd need your savegame to find out what mod is causing this, but it's definitively a problem that the other mod would need to fix.
actually even if the event doesn't fire, the entity should get removed on the next electricity check..
also, my electric-energy-interfaces shouldn't cause this issue with the collision box, as they have the collision_mask "floor-layer" (gonna remove that on the next update cause it's unnecessary)
the "ts refresh" command probably doesn't remove it, or?