That is a nice idea. I suspect that the aliens would wither destroy the base or convert it for their use. If the destroy option remains the in story it might be an idea to have a big tactical mission available for a few hours after the initial loss where you can fight off the forces that took the base and try to retake it before they blow it up. perhaps after every so often a structure is destroyed requiring it to be rebuilt.
After the time period is up the player can then have a couple of days to retake the base by killing off a token force left behind before it all caves in.
It might be nice to have a shadow of the old layout in the base screen showing where things were and if the player chooses to rebuild the structure where it was it take less time to build because the digging has already been done, but costs a little more because the surrounding rock needs to be stabilized.
Another down side would be that the aliens know exactly where it is so if the player starts using it for intercepts and missions they will be able to zone strait in.
