As has already been said, assuming the correct replacement window motor/controller module has been installed. The replacement motor/controller unit may be missing the correct coding for your car - as @Nino has already mentioned.
I agree with @JYSGTI that I'd be going back to whomever you got to do the work in the first place.
Below may potentially help if you get stuck. Via VCDS I've gone into the module on the driver's side door of my UK spec 2009 Mk6 GTI which has fold-in mirrors fitted from factory, and pulled its long coding config.
Small disclaimer: various revisions of controllers and later Mk6 GTIs may have different configuration settings or options to mine, so I'm not guaranteeing my config would work on your vehicle. Plus if anyone does tinker with VCDS I can't emphasise enough backing up/saving your car's config before making any changes. e.g. do an autoscan and save it, make notes of any Software Coding values before making changes and take lots of screen shots! So any changes can be reverted back if needed helping to avoid 'bricking' your car.
Anyway the config for the
42-Door Elect, Driver module on my vehicle is:
Byte 0Byte 1Byte 2