Don't quote me on this but im pretty sure save data is already saved on system memory/SD Card memory. So picking up the digital version of the game it will just use that pre existing save data. While typing this i found a reddit post that says the same thing. https://www.reddit.com/r/NintendoSwitch/comments/6wxkrq/if_i_buy_a_digital_game_that_i_already_have_the/

The wording there is unclear thats why they are asking. It says "should be turned off" it doesnt say it has to be.