Edit: For those that might find this post in the future experiencing the same problem the solution is this: Simply battle wild pokemon until you are able to initiate Pokemon Refresh from within the end-battle screens. The Refresh UI will not show at first - just touch the screen. From now on accessing Refresh from the menu will no longer crash the game.
Newly Homebrewed my DS since browserhax and menuhax was patched to use PKHEX for the first time ever.
I exported the save with JK, added a team of 6 pokemon to empty box spaces. All passed legality checks.
I also added 100 full restores, 30 rare candies, and 400 figy berries.
After importing the save the game now crashes when starting Pokemon Refresh. When hitting the button a party pokemon appears in the refrsh screen with their back turned to you. No menu appears and you cant click or swipe anything. Must soft reset or power down to get out.
The problem persists even after reverting to my original untouched backup save file.