Strikes me as a gross safety violation at the ISS if they're going to alter vehicle software mid-mission.
I'm speculating, but I bet the mechanism to flash the vehicle with new code involves sending development software to a laptop on the ISS, training an on-site astronaut on the use of the dev software, connecting that laptop to the capsule (USB? RS-232?) and pushing freshly built code to the vehicle. As such, the vehicle will likely be powered down or power-cycled during the event.
The International Docking Adapter (IDA) ports that Dragon and Starliner and Cygnus use (and Dreamchaser will use) are supposed to be androgynous, but everything sent to the ISS thus far has been either A or B gendered. I want to say that all capsules have the Active portion of the interface, while the ISS has only a Passive form of the interface. There are hooks that secure the vehicle to the station, and the motors that control them are on the capsule rather than ISS. This is for lifeboat purposes, so that if ISS is compromised, survivors that make it to the capsule can depart the station using the capsule's computers or manual bypasses and not rely on the ISS functioning to disengage from the station.
Now, imagine if Starliner does what your inkjet printer does when it power cycles. Tests range of motion of clamps, or function of clamp sensors... something like that. With the capsule door open and the ISS IDA port open to the capsule, you vent the station and capsule both to space. It's possible there is a manual security lock for the IDA clamp hooks; I would hope there is at least. Something software cannot touch, and only operates manually from the capsule side.
Conversely, if they shut everything at the capsule and ISS and flash the vehicle with the astronauts inside, they are now in a machine that is powered off and at the mercy of whatever is on the laptop and in their heads, with about 8 cubic meters of breathable air to resolve any new problems.
Flashing the vehicle mid-mission is asinine.