Impact of switching is unknowable. Too many variables. It's all guessing. If I were to guess? Pretty good argument can be made it hurt HK. The games will not be equivalent, though, and there's really no way to estimate the emotional impact it'll have at this point.
I tend to lean more towards negative. Unsure of scale. You create alt-history in other games, too. No EU3 or EU4 game goes anything like what's written. However your opponents retain their own in-game story, identity intact, rather than becoming something with a different identity at an arbitrary point. If you told EU Byzantine players that their state becomes the Ottomans or some kinda Mamluk Sultanate at 1650, the community reaction would be much more extreme than what we've seen from the civ community, in my estimation.
Civ is... sorta doing that. Although their game is more abstracted than the EU series from the start, I think it's a safe bet it'll have emotional impact, and I don't think it'll be positive. Those who are on the attack presently aren't really those I see impacted, the greater risk for Firaxis are the players who are interested yet see that interest wane as a consequence, often despite their sincere intention to enjoy the game.