Hey crashmaster thanks for the reply. The shop says they took the CT to another location where they have a Honda master tech and diagnosed it that way.Is the shop you took it to a Honda Dealership? If not, I would suggest that you take the car out of the independent shop and have the Honda dealership take a look at it.
Pretty much everything is tied into the ECU these days including the AC. It does seem odd that after they played with it that it stopped completely. Again, if you don't feel comfortable, take it to a different shop.
They previously saved me $900 because they diagnosed a similar issue to be a bad ground where the Honda dealership wanted to charge $1200 to replace the relay box.
I still think I do need a second opinion but came on here to find out if it was a common issue.