If the clunk is still there on your 2010 e60 with the 6HP19, after the software recode, it doesn't appear software was the answer.

Did someone take the joy ride of their life in your e60 and damage the transmission? How did the clunk surface?

Have you performed all the super obvious activities and none of them have worked?

- worn U joint?
- loose transmission mounts?
- first gear solenoid faulty?
- drive shaft center bearing?
- bridge seal, sleeve seal replacement?
- multiple lifeguard 6 changes?

 

You sure it's not the drive shaft flex disc (giubo). It's a common issue on BMWs

 

Something to know about this clunk. In my case, when I park I set the handbrake firmly, then select neutral and release foot brake. After the car settles I put it in park. On restart, with no tension on the driveline, I get a variable clunk just after the car starts, and the car is still in park. It does not do it when selecting gear afterward. I can select reverse or drive and get no clunk, and I have no loose drivetrain parts despite having over 235k km on the clock. I suspect the transmission momentarily engages a drive mode when the engine starts.

 

I'd like to elevate the car and lie under the transmission.

Then have you start it and listen to identify if there is anything to be learned from experiencing the cluck while being under the vehicle.

Brainstorming:

Can we rig the vehicle to start in neutral and see if the clunk surfaces?

What is you borrowed a friends gear shift selector that fit your car for a minute?