Archipelagates does not use a save system like you see in Skyrim or similar games. The save is just one text file that contains all the necessary info (your appearance, gate lvl, max hp, inventory, unlocked sex positions, unlocked house upgrades, your chests' inventories). So basically every time you load your save the game recreates the state of the game at the time it was saved, just like old games used to do.
If you still need the location of the folder it's: AppData\LocalLow\RalivDev\Archipelagates