Our software update is now concluded. You will need to reset your password to log in. In order to do this, you will have to click "Log in" in the top right corner and then "Forgot your password?".
Welcome to PokéCommunity! Register now and join one of the best fan communities on the 'net to talk Pokémon and more! We are not affiliated with The Pokémon Company or Nintendo.
If you do a complete user transfer from one Switch to another, your saved data should go with it, yes. But just in case something goes wrong I STRONGLY advise creating a backup copy of your SD card data to your computer before you start the transfer process.
From what I've read online, you can transfer downloaded copies of your game to an SD card you bought and put in your Switch. That should include Pokémon Let's Go. Unfortunately, it seems you can't make backups of the save data since save data can't be transferred to the SD card.
You'll have to hope the complete user transfer is executed successfully.
This video doesn't show Pokémon Let's Go save data being transferred, instead depicting other Switch games, but any other game's save data should function similarly.