Hello Mlahdes,
The way to keep counting during the measurement is by putting two parallel loops: One containing the counter Vi's, the other containing the analog input vi's for the measurement and using local variables to communicate between them.
Attached you will find a small example I wrote that simulates what you are doing. In this example, when the number of analog edges is greater than two, it triggers an analog acquisition. You will see also that when this happens, the counters keep on counting the digital edges.
Please let me know if this helped or if you have any additional questions.
Best regards,
LA