Never update an RPG Maker Game by Overwriting the OLD Version, that will more often then not Result in Bugs and double scripts to fire off, and potentially making bugs that won't exist otherwise...
so unless the Developer or Mod Creator say otherwise whit an Patch, then don't overwrite games in that way in general.
game engines like RPG Maker and Ren'Py are well known to have problem whit overwriting in that way.