Hi Kousy!
I'm not shure to have understood exactly... your 2 VIs are executing in parallel, or subsequently?
Anyway, what do you mean by "release resources"? I think you don't need to reset device,
you'd rather stop the DAQmx task in the first VI, (clear it, if you want), and
then start another task in the next VI, reconfiguring M-board ports, and so on; in this case you can reset device (but I think it's not compulsory....).
Let me know if this helps! Have a nice day!
graziano