My sister has it, I am popping down there tomorrow. The screen says it only need to be done once, but I am not sure if it needs to be done once per eShop game or once for the console.
Because so far, they have had the Switch 1 for the past few months, whenever I see a cheap game on the eShop that I think the girls (nieces) like to play, I would buy it and it would install automatically to the console and ready to play next time they boot it up.
I would like this to continue.
If it's hassle moving between the consoles, I would do a lot of reading of how the set up works between owning two consoles, looking on reddit it seems to be typical Nintendo - "this could be straightforward but lets make it complicated just in case someone dares to try and play one game on two of their own consoles"