You shouldn't have to reinstall if you're on desmume. AR codes modify RAM so, you should be able to just restart the emulator. You do need a save already to use the mentioned code. You can however use the code as soon as you can save ingame.
Pkhax has no way to differentiate between a normal and modified rom so you don't need to worry. Just generate mons in the pc and the game will fix the stats upon withdrawal.
This is a bit off topic, but if you go to your profile there is a section for all of your friendcodes/gamertags.
On another note, it's not a good idea to post your email on forums. There are bots that scan for emails to send spam to
If you can find a donor save that has not collected them, you can create new saves immediately before and after receiving them, then comparing the saves with the pkhex flagdiff function and submit the flags for introduction into pkhex by the devs
I know I'm not SkyLink, but you need a bckup to restore a backup. If you never created one, you're SOL. If you do have a backup, do as skylink said, It should be on the microsd card you used with your AR, assuming you haven't formatted it.