When the crown is pulled out, a stop lever/ brake, will stop the balance.
The chronograph parts will still be engaged on the movement side, which is the stuff you see from the caseback.
Setting the time engages parts on the dial side, it should not affect the chronograph parts. after setting the time, push back the crown and it should function as normal. Maybe a little slower to catch back the time since most things are engaged.
Modular movements have the chronograph parts on top of the dial side. still, shouldn't be too much of a problem to adjust the time when chronograph is running.