This might be a stupid question, but I am trying to figure out why my simulated motor seems to have so much more power than my physical motor.

System: 44V and 12A power supply.
High-Power Motor Driver 36v9

The maximum effective voltage I will allow to my motor is 22V, which implies that the highest PWM duty cycle I will send to the the motor driver is 50%. My question is whether or not the max current available to the motor will scale by 50% as well. I.E. if I am sending a 50% duty cycle of 44V/12A does that mean the max available to the motor is 22V/6A?

It’s not a stupid question at all, and I don’t think there is a simple answer. First off, you’re complicating an already non-trivial problem by looking at it from a current-limited power supply perspective rather than assuming an infinite power supply and considering what the circuit will draw. If your load can draw more than 12A at 44V, it might still want 12A at 22V, and the answer to what will actually happen will depend on the details of your power supply. If the power supply can deliver more current than you will ever need, the 12A limit is irrelevant.

How much your load (e.g. your motor) draws will depend on the details of the load and the PWM frequency. The simplest case to consider is a purely resistive load since the current will look just like the voltage waveform. 50% duty cycle will lead to 50% power, and since power is I times V and both have the same shape, each will have to be the square root of two times half the maximum (a factor of about 0.707 instead of 0.5, so it doesn’t equal the PWM duty cycle). However, with an inductive load and a high enough frequency, the current will become steady at the duty cycle times the maximum current.

Since a motor is not just resistive or inductive, I think it will be quite difficult to simulate all the interactions that will determine the ultimate outcome, so if you have the physical motor available, you should probably try measuring its actual performance in your system and use that in further simulations you have to do.