The emissions fix will indeed wipe over any remap you have. There have been some complaints about the update causing issues with people's cars.
https://www.theguardian.com/money/2...skoda-seat-emissions-fix-left-car-undriveable
There's a bit of an exaggeration factor involved as people with a
problem these days will usually complain on the internet somewhere whereas no-one ever posts saying they've had no issues, but issues do seem to be rather more widespread than you'd expect.
My car won't be going in as it's remapped but to be honest I probably wouldn't take it in even if it wasn't.
Interestingly the SEAT TPI on the EA189 fix says the service centre should ask the customer if the vehicle has been remapped (as well as checking for the diagnostic flag for ECU tampering) and seek confirmation that the customer wishes to go ahead with the update.
The simplest solution to avoid it being applied at all costs is to not take the car to a SEAT dealer. I've made the decision to start self servicing my car after seeing how badly it's been treated by SEAT anyway. I've got scratched paint in the engine bay and a couple of sheared bolts too and of course the dealer that last serviced it just shrugged their shoulders when I sent them photos of the issues.