Yes, haxchi replaces the rom within the game. If you decide that you'd rather have the game instead of haxchi, and you have NOT installed CBHC, you can delete Haxchi from Data Management and re-download the game.
As an alternative, you could use Haxchi's sysmenu option to run out-of-region and non-legit games. That means that you could find and install another region's version of the same DS game. Each region's game is a different title ID, so there's no conflict to the system.
Thanks Nexus.
But now I got another problem. stupid me, i install big brain using wup installer and now it occupy haxchi icon. So i deleted the big brain but haxchi wont start and error "nintendo id bla bla" and require me to install big brain. I download it again but error "105-3687" when installing. It led me here but i cant delete .tik coz cannot access "storage_slc" with error "failed to retrieve directory listing". what should I do? kinda desperate now..