Here is a quick fix. Once a base has come under attack it should no longer be able swap modules for the duration of the lock or until disabled. As it is now, it is kinda bogus for a legion to be able to dump all their shields after they are down to zero. Then install more hull and repair. Or really to remove anything and replace it with something else.

These bases are pretty huge so I imagine it should be impossible to do a major overhaul in the middle of a firefight. Imagine being in a battleship in the middle of the pacific. Suddenly the captain comes in over the load speaker. "This is the Captain speaking, there are alot of smaller ships attacking us so we are going to take a few of our turrets and hang them over the side to act like armor instead."

go-go-gadget armored tank!!!

or more correctly...

go-go-gadget Borg Cube!!

lmao