My Dyna doesn't recognise either key fob. I have done all the usual tricks inserted new batteries, cleaned contacts in fobs all to no avail. Question - the computer in need of reboot ( I have tried the old down power reboot) is still not working and I have to put in code everytime I want to start. The computer did get confused recently and I had to down power but it appears OK now again to start using the pin #. 

Welcome to the forum. 

My 2007 dyna has done this 3 times. Even the dealer said he has only seen this issue a few times...electrical interferance. Eg.  Phone tower wifi signals.  This has happened at the dealer own shop.   They just move the affected bike down the road a bit and it starts... Also. Under your seat near the tank. Is your antenna reciever.  Long thing about 4 inches

I have had the issue with phone towers and also police radio towers (VHF or HF radio) with the bike not starting. I can start and ride using the PIN # but this is a pain in the arse to do every time I start n ride. It would appear the reciever for the FOB is rooted so I will have to take it to the dealer so he can buy another new set of sails for his yacht.

This used to happen on my old street bob.