I can tell you that the Owner’s Manual for my Accord stated that a flashing “D” on the transmission quadrant indicated an electronic fault in the transmission and that failure to remediate that electronic fault could lead to mechanical damage to the transmission. I would assume that the Owner’s Manual for the Pilot would have similar verbiage, so the question (to which I think I know the answer) is:
Have you read your Owner’s Manual regarding the warning lights and controls for your vehicle?
If you have never consulted the Owner’s Manual, I can tell you that it is a wealth of information regarding the safe operation and the maintenance of any vehicle, and the owner who does not read this book eventually pays the price in terms of problems that could have been avoided. Even if you have never looked at the manual previously, this would be a good time to do so.
So–I would suggest that you have that transmission checked a.s.a.p., before more damage results, and you should definitely avoid all “chain” transmission shops. There is an extended (silent) warranty on the transmission on many Honda models, due to ongoing issues with their transmissions. In case your Pilot is one of those models, you should really take it to the dealership. While you are sitting in the waiting area, you can start to read that Owner’s Manual!