Topic: How does a system transfer work?

Too make a long story short i have a couple hundred dollars worth of content installed on my 3ds.
When the nintendo network came along i made an account, Immediately disliked my user name and then deleted the account which also without warning deleted all of my ehop content.
i had to call nintendo's customer service to resolve this as i couldn't re-install them for some reason, i'm assuming they became linked to the nnid

So what i need to know is if i transfer my stuff to my new 3dsxl will it all just install to my new nnid or will it try to overide it with my old nnid that no longer exists and delete all my content again?

Well if it's just a system transfer you just go into settings and do the transfer, EVERYTHING get's transfered, you don't need to redownload anything, after you are done the transfer it's just like your old 3DS got a new shell, nothing changes, still got your Nintendo ID, still got your friend code and friends, all saved data is still there so you don't need to start any game over again, all your photos and stuff will be there, you can even use your SD cards fine.

I can't avoid to think you rushed the delete back then, I tried once to change NNID and a big warning popped out about losing forever all the eShop contenent I bought ^_^;

Anyway all that @Undead_terror said apply, just make sure AFTER you made the transfer to switch the SD cards between the consoles (or copy and paste the datas between them if you like) else you won't find your games on the new console.
I'm not sure instead about the old NNID, I think you can always make a new one, but even that must be made after the transfer since anything you did with the new console before the transfer will be lost (if I remember correctly).

EDIT: Just to be clear, you can transfer only the games you own, or for be correct the transfer will only give to the new consoles the eShop datas of the old console which only include any eShop download you made after you deleted the old NNID.

If the nnid on the old 3ds was deleted and your problem wasn't resolved by Nintendo; then transferring your data to a new 3ds will not give you the games back.

Because you deleted them along with the nnid.

If you got your games back from Nintendo, then you should be able to transfer them.