Sounds puzzling. Here is what I would try first. With the Ag Leader system hooked back up, use the manual rate on the right tab/window to set a fixed volume output. If the flow meter starts reading again go to the Diagnostics in the upper right corner, Liquid Product Module, and then Diagnostics in the lower right corner. Watch the flow meter frequency. It should be constant with the rate control in manual. If it fluctuates it is a sign of a bad flow meter, I have caught a couple bad but sorta worked meters this way.

The main pressure has nothing to do with flow on the legacy liquid module. To zero out the sensor reading you need to do the calibration routine for the sensor. This will make it read zero.