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You need to understand that your cryptos are never stored in your ledger. They are always stored on the blockchains, on the Internet.
The only thing stored in your ledger is your seed (24 words + optional passphrase), i.e. your master private key that gives you full control of all the accounts derived from this seed.
To learn the basic concepts of crypto and how the ledger works, you should read and study all the pages here: https://www.ledger.com/academy .
The apps on the ledger are just needed for the ledger to understand the blockchains.
You can remove and re-install the ledger apps at will, this has NO EFFECT on your crypto accounts and balances, which are on the blockchains (not in the ledger).
You can control hundreds of different coins with your Ledger Nano S, if you want to.