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: