ROM hacks have varying amounts of differences when compared to the original game. Changing the savefile structure, and/or replacing pkm/names/stats, etc.
It's probably better to make a separate program.
Another update! Changelog: v1.2.0 - September 23, 2019 (Updated by DeadSkullzJr) - Tweaked some of the text - Added the homebrew application version number to the title in the menu.
RTCChanger NDS (v1.2.0).7z
Don't make this more complicated than it is. I am telling you to do this. ON Modify Pokedex, THEN IMPORT the Pokemon data.
When you do this, they will appear as SEEN AND CAUGHT in your Pokedex.