If you created an account within the ledger chrome app (and sent funds to it), you can easily recreate it after being deleted.
If you click on 'Add account' it will derive another account from your seed. The derivation is always the same.
Means: If you accidently wipe your nano s, or delete your account.. you can just click on 'Add account' and it will add the same account again.
Your issue mostly seems to be a display bug. Did you check your address in a block explorer? If the coins are still sitting on your address and your nano S contains this address..
Then everything is fine. Sometimes there are a few display/connection issues.
You can try to clear the app cache (Click on 'Settings' in the ledger chrome app, not sure where exactly) or reinstalling the ledger chrome app.
Your coins stay always safe and can always be derived from your seed! You can install/uninstall the apps as often as you want.
During my panic of not knowing where thousands of dollars has went, I attempted to reconfigure my ledger to an old setting, which resulted in me returning to a home screen where i did not have any icons. Can anyone help me understand what is going on?
What do you mean with 'old setting'?
Do you mean an old seed (without any coins) ?
Note, that you can always restore your nano S from your seed. If you once recieved coins to an address generated by this seed.. it can always be re-generated again.
