Technically, you
should be able to just write over the Day 1-3 patch files, but it would be safest to just create a new subdirectory and delete the older patch directory once you know the new one works.
Mion (Sonozaki Futago-tachi)
EDIT:
Also be sure you have the Demo patch for the Demo game, and/or the Full patch for the Full game! I was able to replicate the "close immediately after launching" bug when I was running the Full patch on the Demo game.
But if you still have problems even though you're running the right patch in a new subdirectory, be sure to let me know.