Initialising the Nintendo Switch console 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.
If you have save data backups stored using the Save Data Cloud service, you will be able to download them once you create a new user and link to it your Nintendo Account.
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 console. After initialising the console, you can create a new user and link to it your Nintendo Account.
Your Nintendo Account contains your Nintendo eShop purchase history and balance. By re-linking your Nintendo Account after initialising the console (whether to the same console or a different one), it is possible to redownload any software or DLC purchased using that account.
If you are not connected to the internet while initialising the console, it will remain registered as the primary console for your Nintendo Account.
You can also initialise a Nintendo Switch console without deleting save data via recovery mode, which will retain save data and user settings on the console.