Being able to 'backup' the games downloaded directly from the Nintendo servers is the main reason why I use CIAngel instead of FreeShop.
You see, with CIAngel one can choose to create CIAs off the games it downloads from the Nintendo servers. I then move the desired CIAs to my computer.
This does not exactly apply to your case because you already have those games installed, but you can start creating your 'backup library' today.
Note that recent games require a 'Seed' (it is a sort of token that updates the title database) before being able to run (they either get stuck in the title screen or cause an exception error which forces a restart.) Luckily, FBI can easily fetch these 'Seeds'.
'Seeds' are the one thing that prevents offline-only installation of games.