Title is a bit cumbersome, so will try to break it down ...
If you have a constructor ship that has multiple constructor modules, and you take it to a starbase to upgrade that starbase, but that starbase has only one available upgrade, the entire constructor (all of its modules) will get consumed making that one upgrade. There's no constructor left to move to upgrade another starbase.
This is inconsistent with the fact that if you have a constructor ship with multiple constructor modules, if you take it to a starbase that has more than one available upgrade, you can upgrade one module on the starbase, and the constructor will still remain (with one module consumed) that you can then eject from the starbase, move to upgrade another starbase or build a new one or shipyard, etc.