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Data acquisition stops during single pulse output (long pulse = 10 hours) [NI USB 6210]

Hello, guys. I am facing some problems when trying to create a VI for data acquisition and controlling a relay.
I want to measure the voltage of a battery during charge and discharge. During the discharge, when the voltage falls to a specific value, a single pulse from a counter turns on a relay that inverts the polarization and starts the charge. This pulse lasts all the charge. When the pulse ends, a new discharge begins. The problem is that while the pulse is being applied, the measurement does not work, but when the discharge starts again, data acquisition works fine. I have tried continuous samples, N samples and so on, but nothing worked. I am a beginner on LabView so any advice will be great. Block diagram and VI files are attached.

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Instead of a counter, use a standard digital output.  I am pretty sure the counter task must finish before the loop will iterate.  If going the DIO route, use the Elasped Time function to decide the state of you DIO.


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