Even if they do reflash it .... they shouldn't do any more than wipe off the Superchips map and put their latest version on.
It is, effectively, all you are doing if you put your car back to standard using the Bluefin device - it wipes the ECU and reflashes it with the new file.
It should have no effect other than meaning you would have to re read the new VW file, send it to Superchips and await their 'new' version to work with the new codes.