Hi GivenRandy-
It seems like you have to distinct questions- whether a self calibration can be performed during operation and if autozero readings during operation will be able to remove the offsets from your readings.
First, in order to perform a self calibration for the board you will indeed need to stop the acquisition before calling the function.  Once the calibration is complete you can restart the task.
As for the autozero functionality, if your calibration changes then the autozero values will not be correct.  In fact, they will be skewed by the same amount as the actual channel readings and the subtraction will not have the effect of removing the true offsets.
So, if you plan to run self calibrations during operation you should probably also perform an autozero subsequently after each calibration.  To reiterate, you will definitely need to stop your acquisition to perform the self calibration.
Please let us know if you have any additional questions.
Thanks!
					
				
			
			
				
	Tom W
National Instruments