Paying For Dirt Bug
If you take down a facility and leave bare dirt, you will continue to pay maintenance on it. But not at the old rate; filling the hole back with dirt means it needs special attention at all times by specialists. In fact for every square of dirt you have that used to be a facility you will pay $80k/month. Thats $320k per hangar you take down.
There are only two known ways to stop paying this premium: 1) completely dismantle the base, or 2) build over all the spaces that you have vacated. In fact as soon as you start building the new facility you stop paying the premium, as well as not having to pay the cost of the new facility until it is complete.
Note: If you start a facility and change your mind before it is complete, after the time it would have completed you will start paying this $80k premium!