Hi Martin,
Reseting the DAQ board will reset all signals. However, there is a small capacitor that needs to release its charge. If your source impedance is high, it might not "reset" as instantaneous as you would like. It will morelikely "float" to ground. This might do the trick for you though. As for the PXI switch card, IVI supports a "disconnect all" function which will disconnect all inputs. Reseting a switch card will usually put it in a default state (Normally Open is the usual state) but this depends on your switch card. This switch reset/disconnect might be your best option for your application.
Have a good day.
Ron