All save data is stored here:
%AppData%\..\LocalLow\RalivDev\Archipelagates
Updates do not clear data.
The Itch app allows you to do some really strange things with installs using privacy sandbox mode, which some people have done and found trouble when reinstalling. All data is normally stored at:
%AppData%\..\LocalLow\RalivDev\Archipelagates
If you have enabled Itch sandbox mode (a data privacy feature itch offers to do nonstandard installs) I am afraid I can not personally account for how and where itch stores your data.
The list is scrollable if it is too long. Every NPC the game can see should show up. There may be a bug, or you may have files that aren't reading. Check your custom NPC directory here:
%AppData%\..\LocalLow\RalivDev\Archipelagates\npcs
(paste into windows explorer)
EDIT - There is a bug causing your issue! My apologies, I'll patch it soon
Ack! I am sorry to hear that, I always recommend the Itch app, and use it myself. I am glad to hear running the exe works for you, but that is frustrating about the app. Hopefully it was something in particular about your setup that caused the app to fail, and not a problem more people will run into.
I had to delete a post here. I try to never do that, but it was pretty aggressive misinformation.
Steam declined to sell Archipelagates due to their belief that the game's characters in some character create configurations look too young. That's the whole story. I did my best to limit the character create so that would not happen, but they were not satisfied, and they have every right to decide that. I am sorry to everyone who wanted the game on Steam. I hope to do better with future games.
I am not at all bothered by folks asking by the way. I just get tired of explaining, sorry. And if the person that wrote the comment I deleted reads this, please don't make up stories.