Hello. Not sure since what version that this issue has existed (most likely since the very first release), but I just noticed a problem when trying to play one of the affiliated games (linked on "Another Games" menu in LNS), Glory of Holly.
LNS seems to create & use the folder named "GloryofHolly-1747817158" within RenPy Roaming-AppData folder on Windows. Looks like you might have forgotten to relabel/rename the project under settings?
This leads to the problem where the saves overlap between the two games. I presume this is going to cause major issues beyond the saves of either game showing up on both - because there's going to be only one shared 'persistent' file.
I hope you'll be able to address this soon; I expect you're going to have to find a way to address players' saves as well, if/when you deal with the project renaming. Good luck.