Random Encounters Menu Option

A final note; if you use one of the three hacks you'll need to restart a new
game to have it work correctly, because the correct SRAM initialization is
done at the beginning of the game. An alternative is to use bsnes+ debugger,
load a game and before entering the main menu go to debugger -> memory editor,
then type 7E1E1F and edit the value there to a value between 00 to 01 for
the on/off options hack and 00 to 03 for the multi options hack.

What happens if you do not start a new save?  I'm about 10 hours into a TWUE playthrough, and I applied the on/off options hack, and it seems to work fine as far as I can tell.  I was just wondering if this will cause issues later on?