Is there a reflash that the dealer should do when changing mufflers like the stage I reflash you get on the standard bikes when you go to the stage I air intake and mufflers? I know, it's probably a stupid question, but I'm a newb with the CVOs.
The CVO's are already "Stage 1" from the factory, so I doubt there is another street legal calibration they could download to your bike.
If all you are doing is changing the mufflers, you should be safe for the short term. The stock engine management system has the ability to make small corrections to the fuel settings automatically as a way to compensate over time for changes to things like fuel pressure, injector flow, air flow due to air filter maintenance or lack thereof, or changes in the oxygenate content of the fuel. This automatic system is not meant to compensate for modifications, and I wouldn't recommend making changes and never getting the tune updated. But for a minor change like the one you propose, you should be OK until you get the bike tuned. As for the decel pop issue, that has a lot more to do with the design of the muffler you choose and how well you avoid any air leaks when you install them. I recommend using the original equipment style clamps, not the narrow band clamps folks like V&H include with their pipes.
Jerry