[Al Skierkiewicz]

Chris,
The equivalent loop is Vemf-Imotor*Rmotor+2.5volts >> Vbatt for the diode(s) to conduct. In terms of an equivalent, think of the EMF as a battery with the positive lead connected to the postive lead of the battery through the motor internal resistance, the diodes with cathode connected to the positive lead of the battery and the circuit resistance as a series circuit. Current will only flow when the EMF exceeds the voltage drop in all the resistance plus the forward diode drop of both diodes in the FET strings.
My contention is that this will only be the case if the inductor creates a spike and then for only a very short time. The path only exists for the period when the voltage is jumping the gap between segments on the commutator on the trailing edge of the commutator segment. This occurs because or the collapsing magnetic field of the winding just opened not because the controller has gone to zero output. Since there is no sync between the segments and the controller switching frequency, the inductive spike occurring during the off period of the controller is random and unpredictable. In fact even that repetition rate is variable with motor speed. So for your purposes, when the controller has gone to zero, the sum of the EMF and wiring voltage drop must exceed the battery voltage plus 2.5 volts for current to flow. Even if the lowside FET is still turned on, the junction will be shunted by the diode when it is forward biased. My belief is that the EMF won't exceed this unless the system is receiving external force to drive the motors faster than they were turning during the controlled "ON" period. I believe you can sample the EMF during this period but must account for those times when the diodes are forward biased and supplying current to the battery. Don't forget that the battery internal impedance is 11 mohms but the DC internal is lower. I think you will find that several samples over a defined time period will likely give you accurate results.