Can't "flush" the Allison really. 

Simplest thing is simple drop pan, replace internal filter and fill back up, should take 7 quarts or so with shallow pan which all of them have unless someone changed it.

Any Dex III fluid will work in them, only need Allison approved fluid for an Allison warranty which you do not have with a GM truck. Change sometime between 50-100k depending on work you do with new internal filter. Gasket is reuseable. 

Spin on should be changed ever 20k or so and clean the magnet.  What filter did the guy use? is the magnet blocking holes? I thought all of these were off market by now but that would be an issue, all of the fluid has to go through that filter. Did he change internal filter?  Possible internal filter is not sealed or fell off. Is the fluid level correct?