Does cold galvanizing compound restore the rust protection of a galvanized duct?
The zinc coating on the galvanized duct work is not in any way required to control corrosion of the A-coil.  Isolating the unit from the duct work is commonly done in the trade to provide vibration isolation.

However, sandwiching corrosion under a sheet of rubber that is not fully adhered may not be a good idea.  Moisture may become trapped between the two layers.  Also, it is generally not acceptable to place flammable materials such as rubber inside of duct work.  You would likely be better off painting or cold galvanizing the duct after applying your phosphotizing chemical.  If the condensate drain on the new fan-coil is correctly installed and kept clear, very little condensate should reach the duct.