Visitted the dealer yesterday. First, The technician confirmed that the 2nd symptom, the clunk when the gear engages, is also caused by the the fact that the transmission is in limp home mode at the moment, and it is directly engaged at 3rd gear. He said that it seems to be a heat related problem based on the fact that it happened after stopping the engine for a while and at local drive . It can be caused by any thing from low fluid level (they checked it before and it is not the case), a clog filter (they did not change it when the ATF was flushed at 39000 mile), etc. The problem can be more severe according to the code of P7017, that inicates the whole valve body needs a replacement. Replacing a valve body is a $2200 job!
I may ask them to change the filter and re-flush the transmission first, which is at around $550.
The ATF level in 7G-Tronic transmissions, is determined by visual inspection of the draining oil stream from oil pan.
Why would you want to replace the oil when you did that previously? Your transmission did not suffer any mechanical damage. So you don't need to replace the hydraulic unit (valve body), no matter what the dealer says. The Electrical Unit (electronic that mounts on top of the body) inside the transmission might need to be changed, but as I've said, you didn't mechanically damaged the transmission so any electrical faults are directly related to oil level.
Heat related problem that I am referring to, is directly related to the sensor inside the transmission. The thing is, your oil level (which is probably low) doesn't enable it to measure the oil flow correctly. Why? The oil at high temperatures expands, and becomes rarer, so if you lack some small quantities of oil, it wont flow correctly over the sensor and it will go into limp mode.
Before you replace the filter and flush the transmission, add 0.5 liters of ATF. You wont do any damage to the transmission, and will eliminate the possibility of low oil level.
That is my advice. Best regards
PS. Have you asked the dealer about the adaptation?