Starbase upgrades

[Suicide Junkie]

Its only adding a spaceyard or colony module that is a problem. You're free to remove them at any time.
Still, the fact that it takes up 400kt and you'd have to have a spaceyard elsewhere to have built it in the first place really defeats the purpose.

Now, if you were to include a repair bay, and place BSYs at strategic locations along the route your ships take, you could have them retro as they pass the BSYs, and repair the new components as they move towards the next BSY and eventually your front line combat zone.