If you've downloaded my build, just follow the instructions in the included "README" file. The section "Breaking the encryption" details how to do the initial breaking, which only needs to be done once. Then, the section "Breaking the encryption for more boxes" details how to fully break the encryption. Basically, you do this:
- Create save1, save2, and save3 according to the instructions
- In the Options tab, load save1, save2, and save3 into File 1, File 2, and File 3 respectively
- Click the higher "Break" button (the one above the File 1 slot)
- Now create empty, full1, and full2 according to the instructions
- In the Options tab, click "Folder" and select the folder where you put empty, full1, and full2
- Click the lower "Break" button (the one above the Folder slot)
All that only needs to be done once. After that, you can open any save in the SAV tab, and you should see all Pokemon with no ~ markers.