Skoda Citigo e IV power window issue

It sounds as though you've encountered an issue with the EEPROM within the window regulator motor itself. Replacing the battery on a Skoda Citigo-e iV can indeed cause control module amnesia. Have you performed a hard reset of the car electronics? Have you checked all fuses related to the power window system? Did you disconnect the old battery and connect the new one immediately, or did the car sit without power for an extended period?

I haven't done a hard reset yet. Where exactly are the fuses for the power window located? And yes, there was a bit of a delay between disconnecting the old battery and connecting the new one. Maybe 20 minutes?

Indeed, the delay could absolutely be a contributing factor. It sounds like the volatile memory within the window regulator control unit has lost its adaptation settings. While fuse location is dependent on the specific vehicle configuration, the delay in power most likely corrupted the non-volatile memory. Recoding the window regulator with appropriate diagnostic equipment (e.g., VCDS, ODIS) is now necessary. I'd suggest visiting a workshop equipped to handle car electronics to perform the re-initialization. Continuing to attempt DIY fixes without the proper tools could potentially exacerbate the issue.

Took it to the workshop, and they confirmed the need for window regulator re-initialization after the battery change. The service set me back about 290€.