"The upper city was just the parts of the upper city found in the final battle" is much simpler than "Larian lied several times about a secret scrapped section of the game that would explain away the incompleteness and also held the key to fixing Karlach, despite the lack of datamines pointing to any of these plot points or locations, and it was all deleted within the span of a month after its apparent development was highlighted".
Unless I'm missing info, the Emperor wasn't a change made within a month. It was obviously after EA, but, for reference, IIRC Theo Solomon (Wyll's new VA) started working on his character in 2022, so did Karlach's, IIRC. Both of these characters feel very rushed and they're still the work of almost 2 years, and they're not necessary to the main plot, unlike a new section of the game. Next to that, a month to delete all traces and ramifications of an entire new location is insane, especially after having apparently tried to showcase it's appearance in the game.