It sounds like something needs clarification. In addition to the local saves folder in each copy, there's a system saves folder in
%APPDATA%\RenPy\
. So, for example, any and all copies of Week 1 DM have the same system saves folder,
%APPDATA%\Renpy\Ecchi Sensei
. That's what the unmodded version is seeing, not the modded version's local saves.
The bottom directory is set in
game\menu\options.rpy
. So if you followed
Latecomer's advice, you could make it so the modded version used
%APPDATA%\Renpy\Ecchi Sensei (mod)
instead.
Things get a bit more complicated with Week 2 due to the method used to automatically "import" Week 1 saves: