How did you delete them in the first place? The simple update has no effect on either of those things, as per many other reports of people updating to 11.3 with Luma+A9LH. So you must have done something else.
Lets recap a little.
1) Updated to 11.3 (black screened).
2) Used decrypt9 payload to restore 9.2
3) Updated to 11.3 again (blackscreened)
4) Updated luma and it worked.
Now when I hit the badges Icon it tells me "This feature cannot be used, because you dont have any badges yet"
Tried to download the badges app to see if they popped again... nintendo store tells me I need to create an NNID...
The files must be there somehow but the system doesn't see them? I dont know
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I dont think relinking my NNID will bring them back since Nintendo has zero records of what badges you have and what not.