Ideally you will want to know what the software is doing, fix it, clean it up, and document it. OTOH you are reasonably certain that the software used to work and "something changed".
OK, did you try playing with the settings for the flowmeter? I particular did you look carefully at P.14 in the documentation?
There are a number of settings you could change to attempt a quick fix, with the caveat that this is still just a stopgap solution. If you go this route be sure to note the current settings before making any changes.
Also you should get a multimeter and test the connections (wires) and that the power supply is still working. . .
Good luck,
Eamonn