ANSWERED - While preparing an example that demonstrates this problem happening I stumbled upon what was going on and it makes sense. The watchdog counter does indeed cease to count down when its prescaler is changed, but not forever. Most likely long enough to cause a timing problem and watchdog reset if you are using the window feature.
Imaging the prescaler is a down counter that decrements the watchdog timer each time it reaches zero, then resets itself to the prescaler value (-1). So for a prescaler factor of 16, it decrements the watchdog counter every 16 clock counts. Now, say this prescalers counter is at 15 and you reduce the prescaler value to 4. You are expecting the watchdog counter to now decrement every four counts. But, for the first period the prescaler has to count all the way down to zero so it will take 15 clocks before the first time the watchdog counter is decremented. During this time the watchdog counter remains at a constant value. Kind of obvious really after you think about it, standard timer behavior without shadow registers.
In my case, this additional 11 counts equates to 5.5ms. This would not really be an issue if not using the window function. A risk that an expected watchdog reset could take longer but. If using the window function then you rely on another timer (tick count based maybe) to let you know if it has been long enough since the last kick to be allowed to kick again. So, you kick the dog, and think you are not allowed to kick it again for say 10ms, but it got stalled for 5.5ms by the prescaler change. So, when you go to kick it after 10ms, it has not counted down enough and you kick it inside the window and BOOM!
I have attached a minimal example (STM32H753ZITx and STM32CubeIDE) showing this happening for future reference. If you place a breakpoint on the line wdogslowed = 1, then after it is hit, place a breakpoint on the line 155 lastWDogKickTime = now then you can watch the WWDG CR counter not decrementing in the SFRs view. Eventually you will see it start to decrement again.