When replacing a project flow, it will create new variable Ids behind the scenes so all subsequent references to variables output from original project flow get broken. Having a feature that allows a variable to be replaced (like a find-replace on text in a doc) would mean swapping in a new project flow would be much easier to handle and no need for all the manual variable updates (which can go wrong).
When variables break, it would be good to somehow show the name of the removed variable so that when replacing, you know what the variable used to be called.