I have no harsh downshifts with my 03 4.6is... and (knock on wood) have had zero indications on any transmission problems as of yet, at 95,000 miles. I did reprogram the DME and EGS with the newest progman software back when I retrofitted the trailer module, just because I could

, but had no problems before that either.
If it is all customer pay, you could always ask them for a price to do a tranny pan drain and fill with filter replacement, followed by reprogramming with latest progman software if they still have an operational progman terminal, otherwise ISTA-P programming of the EGS.
A non integrated BMW like the E53 should only cost 1 hour labor to program since it won't need to program everything else with it. And the transmission drain and fill with filter will be a couple hours labor and the fluid is expensive per quart, and you will need about a gallon and a half.