I had the same problem ever since I updated to 10.3, it would just error instantly, never found out what was wrong.
But I found a solution to the problem.
I made another emuNAND from sysNAND, and updated that, which worked fine.
Then I dumped these files from the broken emuNAND using GodMode9:
/rw/sys/LocalFriendCodeSeed_B
/dbs/ticket.db
/private/movable.sed
And the entire ID folder inside of /data (the folder with sysdata and extdata inside of it)
e.g. /data/5090d9ef583f2517d8f0b192a0daa3eb
Then I deleted the ID folder inside /data from the new emuNAND and injected all the old files into it.
That got all my old data transferred to the new NAND, including NNID, friend code, friend list, Mii Plaza data, all my installed titles and savegames. Updating works fine now.
Your issue seems to be the same so this should work for you as well.
If you have the NAND with all your data on it either as emuNAND or as a .bin backup on your SD, you can mount it in GodMode9 and transfer files directly to your 11.0 NAND, without having to use the SD card as temporary storage, that's up to you though.
Pics of the files I dumped: