All digital modeling has a small gap when switching scenes or presets that involve changes in the settings for amps or drives. They have to let the “circuitry” settle down otherwise there’d be a burst of unwanted sound, so the signal is muted, the settling occurs, then it’s unmuted. Depending on the processing speed and algorithms and what is changing, the gap can be more or less noticeable.
Analog/tube-amps/switching amps have a gap also. These days they use tiny relays which toggle very quickly, and tubes are able to naturally transition their sound so it’s not as noticeable, but back when we had mechanical switches that controlled the channels we’d often get a loud “thump” when changing channels or enabling boost. My Mesa IIB and my hotwired original Blackface Deluxes did. We accepted that as the price of the new technology and didn’t switch when sustaining a note or chord, in other words, we provided the muting manually.
Typically, to work around that, when using a modeler that allowed dual amp blocks, we’d use a mixer block connected to both amps in parallel, controlled by a foot controller to select which one was being use at the moment, as was said above. Your choice of running two amps in parallel and switching both at once is the same problem as switching a single amp block, the muting occurs but you don’t have the option to fade between two running amp blocks.
Cliff figured out a way around that a couple months ago. It required adding a bit of additional code to every block but the results are really impressive. Transitions between presets and scenes are much smoother. Amp blocks don’t have to be in parallel nor do we have to use a mixer or multiplexer block to select the running amp. Smart people are good to have around.
It happens but it’s not as noticeable. If I remember right it’s tied to the gain level switchover between the two amp settings.
Turn the thump setting to 0 and it’s disabled. Scene switching doesn’t affect the tone. The speaker impedance changes are going to be harder to work around, but you can update your firmware and see if the sound differences are what you want and keep the upgrade, or roll back to your previous firmware. Be sure to make a backup of the presets you are using first, and remember you’ll need to update the Edit app too when rolling forward, and to restore the presets if you roll back.