This is the method I use to update games and I haven’t had any issues.
1) Select the game(s) you want to update from the sx os menu so it puts it on the main screen.
2) Turn off the switch then remove the sd card.
3) Boot into ofw.
4) Select the game you want to update and press + to update. Note: Update data will be installed on internal memory because the sd card is removed, thus saving precious sd card space.
5) Turn off the switch and insert the sd card.
6) Boot into cfw and select the game from the sx os menu and load it.
7) Enjoy playing the updated game.