Okay, finally got done with the whole process, now the transfer. How do I restore the backup to the new card without putting it inside a 3DS(you didn't specify which) and when put the files in from the computer between cards, won't that interfere with some of the homebrew apps(after following the process you linked)
OK, so you have:
1. A large capacity card currently in your O3DS that you'd like to use in your N3DS (hereafter known as, 'old card')
2. A random smaller card currently in your N3DS that you'd like to give to your O3DS (hereafter known as, 'new card')
Swapping cards involves:
1. Moving the emuNAND partition on the old card to the new card
2. Swapping the files over
*EmuNANDTool is used on your PC, emuNAND9 is used on your 3DS, I'm assuming you are using updated sysNAND not emuNAND on your a9lh N3DS*
Steps:
0. Delete enough stuff off the O3DS so that its stuff can fit on the lower-capacity new card (plus less stuff means more likely to be successful in transferring)
1. Use emuNANDTool to backup the emuNAND partition on the old card
2. Backup all the files on the old card too
3. Use emuNAND9 to delete the emuNAND partition on the old card
4. Backup all the files on the new card (all the a9lh stuff). Keep this backup safe, don't delete it!
5. Create an emuNAND partition on the new card if it doesn't have one (using emuNAND9)
6. Restore the emuNAND partition from the old card to the new card using emuNANDTool
7. Copy the backup of the files of the old card to the new card
8. Put the new card in the O3DS and check it works fine as expected
9. Copy the backup of the a9lh stuff to the old card, put it in your N3DS and check it works fine as expected (don't delete backup)
10. Initiate system transfer.
11. Pick wireless data transfer when asked
12. Be prepared for a long wait (if it gets stuck for more than 6 hours and the little Pikmin aren't doing anything, you'll probably have to start again. Turn both consoles off and on again, the O3DS will still be fine, but delete more stuff off the O3DS before you start again)
13. If the N3DS fails to start up after it restarts itself, copy the a9lh stuff from the backup onto its SD card (not the Nintendo 3DS folder, just stuff like aurei and a9lh.bin etc). Whether it works or not let me know, my a9lh transfer was from N3DS to N3DS and I didn't get the wireless data transfer option.