Convert from an input pulse frequency to output another in near real time?

So why not just count pulses? It's super easy to measure volume that way because it equals v/step * nsteps.

To account for the non-linearity you would simultaneously measure each pulse interval and apply the calibration factor.

The only thing I can do is measure the flowmeter it was attached to using a pulse generator.

That's actually just perfect, it will yield a calibration table.