Actually I can confirm that on the dexnav it'll just show the regular available pokemon. When clicking on one it'll search for that pokemon, but as the encounter reference table has been altered a search for i.e. Mew pops up instead. Perfectly "normal" for as far as it concerns the game.
Furthermore, as it is an edit on RAM level rather than on ROM level, leaving petalburg woods and re-entering it resets the encounters to normal ones.