Allison strictly recommends against flushing a transmission system. Just do a drain and if changing to an approved TES-295 fluid, do a double drain and refill. The method is on this forum under my thread: "Former Allison Transmission Fluids Engineer".
Bucketlist,
For two reasons: First, we ran a test where we "doped" the fluid with 500 ppm (parts per million) manganese. We did a normal drain and a flush using this doped fluid and found little difference in the amount of fluid actually exchanged using the two methods. Also, if you're not careful when using the flush method, you can potentially starve the pump for fluid and damage the pump. It has happened before.
That's why Allison does not recommend flushing. Can it be done and not damage the pump? Yes, I'm sure it can; however, if you did damage the pump, you've trashed the transmission and Allison will not pay to have it repaired. Just use the standard drain procedure (or the double drain if changing from a DEXRON-III product to an Allison TES-295 product). It will be much more simple, less messy and a whole loss less risky.