It's hard to say for sure, but I believe if you have been setting VID and ECID simultaneously for a while... I believe that Adobe should already associate those two together in their backend....
The only way to know for sure is to test...
I would try using an isolated QA/Dev suite... do some very specific actions with the before, then do an upgrade and do some more very specific actions..... it will probably take about an hour for the data to process... but you can check if your testing rolled through as one or two Unique Visitors.
The things is, when Adobe decided to switch from the old users ids to the new user ids, they would have done so with the utmost care to try and maintain the same users (and keep the chaos to a minimum).... but individual implementations could still causes issues.
When we made this change in our apps, it was a complete app rebuild, switched users to ECID AND switched the users into the global tracking suite... so really didn't have a chance to try and maintain users... but I do know that the website moving from VID to ECID was pretty smooth (I don't recall any big disruptions in the UVs... but it was about 4-5 year ago... I might have forgotten)