Control software for three phase induction motor
Most benchtop oscilloscopes enter one setting at a time. This way during the configuration the oscilloscope will display garbage because it is using partly old and partly new settings. Then when the configuration is complete it will display the desired waveform.
Oscilloscopes have a concept known as arming the trigger. This is very clear in Single shot mode. Arming the trigger gets a single acquisition. In Auto and Normal modes, this is still the case but the Oscilloscope automatically arms the trigger internally. The catch 22 is that the trigger is not armed immediately after the completion of the previous acquired waveform. There is a delay for processing the data.
What you can do is use the same behavior. Have the ISR check if the trigger is armed. If it is armed then read in the configuration. Set the routine such that the very first thing it does is disarm the trigger. Then change the configuration. Then rearm the trigger as the routine exits.
While the trigger is disarmed just don't do anything in the ISR.