Best to think of it as multiple "apps" on your ledger...
You add and/or remove them using the Ledger Manager:
The Ledger Nano S is somewhat space limited and you can only have 4 or 5 "apps" loaded at once, however you don't "lose" anything if you uninstall one of the apps and then reinstall it... UNLESS you reset the device... All the "apps" use the same seed as the base for creating their addresses etc... so you can uninstall the BTC one, install LTC, send/receive LTCs, then uninstall LTC and reinstall BTC and continue from where you left off...
It can be a bit of a nuisance if you use a LOT of different supported coins... but it isn't impossible.