Matt, I'm definitely in the realm of "don't touch the tranny if it's working correctly" thought of mind. If you do, I would only drain, capture and strain the fluid. Replace the filter and return the original fluid into it.

I trust you do a brake system flush every 30,000 miles, right? Differentials and transfer case at 100,000 miles.

2002 X5 3.0 259,780 miles
2004 325i 115,000 miles