There are a few different software realease on the climate systems and these can be uploaded by Examiner, I reckon that the panel and climate ECU need flashed with the same software. You sometimes need to try a few versions till it works properly.
You also need a proxy alignment (or may just need this) as the odo is flashing.
This is poor show for an auto electrical shop, as you would have the same issue with a Merc, Audi etc. etc. its not unique to Alfa.
Youve paid the diagnosis fee once, as far as I am concerned its not your cost from here on in.
If its any consolation, I dont think the original problem was the panel, its ore likely a re-flash of the software that was required or an issue with the fan-coil heating box itself.