If I suppose that the flag is cleared immediatly at the begining of the ISR(){} routine, the only way to change the conversion channel inside of the ISR routine, is writting 0 to ADATE, for stop the auto trigger, change the channel, activate the ADATE again and exit from the ISR
What is the ISR? There are at least two option, TIMER and ADC_vect. If you are starting conversion by timer, you better to trigger ISR(TIMER) to do a MUX change and data store. Even conversion would be already started before you get in the ISR, delay is a constant, data you taking is always
"stamped" 1 cycle of the MUX settings back.
With ADC_vect there would be less time for MUX to "settle" at new channel. That actually important on fast sampling rate. What is yours?