Initializing the Nintendo Switch will remove the following data:
All data in the system memory, including software, save data, screenshots, and user information will be deleted, restoring the console to factory settings.
All software saved on the microSD card, except for screenshots, will become unusable. (Data on the microSD card will not be deleted.)
Any Nintendo Accounts linked to the console will not be deleted, but they will be unlinked from the system.
Your Nintendo Account contains your Nintendo eShop purchase history and balance. By re-linking your Nintendo Account after initializing the console (to the same system or a different one), it is possible to re-download any software or DLC purchased using that account.