Allison is (I think) the only tranny in it's class with a spin on filter. So it gets replaced, but the internal one doesn't.
But I didn't think it needed to be done at 50K. Where are you seeing that?
Edit: Ahh. They changed fluid at some point to one with less life. So 50K if using GM fluid. External filer at the same time and don't touch the internal, unless doing a full overhaul.
http://fccc247.com/3%20Chassis%20Vendor%20Information/Allison%20Transmission/Allison%20Transmission%20Fluid%20and%20Filter%20Change%20Recommendations.pdf
