You know Ive been wondering the same question.. My guess is that you backup your emunand with the emunand tool, copy all the data from the SD card to the PC, Insert the SD card into the N3DS, format emunand, inject the backed up emunand, copy everything from the SD back to it and boot into emunand with all your .cias working.
This is my theory and it may be a bunch of BS as far as I know so if someone with more knowledge can confirm if this stands it would be awesome.
Already answered here: https://gbatemp.net/threads/emunand-to-emunand-system-transfer-sucessful.378549/
There's also a thread about blocking Nintendo's update servers but I couldn't find it.
EDIT: I should mention that a system transfer with installed CIA's will not work. You will need a backup of your Sysnand before you unlinked AND before you installed any unpurchased CIA's. I have two SD cards for just this reason - One without installed CIA's so I can get to the eShop and one with installed CIA's for gaming.