I agree with you, DGALLUP. We use N-Heptane to flow the injectors, and Viscor 120B to lubricate the injectors. Bosch ans Siemens use the same.
You are correct - you cannot accurately flow test an injector if the filter is not in place. Our machine (New Age) allows the user to flow the injectors exactly as they operate while in the vehicle. We can change the fuel pressure, the pulse width of the injector, and the simulated RPM.
That being said, we replace every filter when we recondition injectors. We remove the filter prior to ultrasonically cleaning the injector. We then back-flush the injector, while lifting the pintle off its seat. This allows any internal debris to exit through the large orifice at the top of the injector. We install a new, OEM filter, then proceed with our testing.