I usually take the need to relink a subVI in every location to examine that location and make sure all the connection still make sense with the changes I have made. I can see how there might be some instances where you know for sure there is no actual change across all uses, but at least for me that doesn't happen very often.
There is a way to do this. Do a "Find All" on the VI that needs relinking, and do a "Replace All" by selecting the new VI. This should be a required step anyway... when you have all the instances of that VI in a list, it's a good opportunity to check every instance (or at least spot check if you have dozens or hundreds of that VI) to make sure things lined up like you intended. (Edit: As jmorris said above!) Prerequisite: all instances must be in memory (read, open the top level and any dynamically called VI's).
