I do not believe that you can test frame flex losses with two power meters. And subtracting two big numbers is only half of the problem.
The bigger problem is that the front power meter does not accurately measure the power input into the system. Correct me if I am wrong, but it computes the power from measuring force and pedal position. However, the latter is measured relative to the bottom bracket. Therefore, whatever number your power meter gives you it is already your power minus the loss.