Sorry but I hadn't received a notification to this post of the replies

Thanks to all those who have replied

I fully understand what the explanation is, but another question has now occurred to me.

When a manufacturer has an update for the Ecu, if this update likely to make changes to the Engine Ecu only or could it also make changes to other systems perhaps controlled partially or exclusively by the engine ecu as well i.e. Braking systems, traction control etc.

I just got to thinking that could there be a case whereby an update it to do more than just an engine mapping change?

If Ecu updates only affect the engine mapping then the suggested route as detailed above by both Chip and Nick would surely mean that once a remap had been carried out any changes made by the manufacturer most probably wouldn't be an improvement on the custom map therefore not necessary.
And a notification to the dealer 'Not' to make changes to the map would a wise move and hopefully prevent any changes being made.