First of all, do not panic, as your funds have not disappeared. The Core wallet uses the BIP44 path which is used as a standard for many wallets. Some users when first using a Ledger create addresses under the Ledger Live derivation path and Core will not read those currently, but will in future updates.
What do Derivation paths and addresses have to do with this?
When using a Ledger Nano X/S, one must understand that there are different derivation paths. Each derivation path can create wallet addresses unique to that path.
If you have multiple accounts within your existing Metamask wallet, the primary address is the same on both the Ledger Live and BIP44 paths, but any additional accounts will have different addresses as shown below.
To put your assets into the correct BIP44 wallet addresses so they can be visible in Core, just follow these steps.
1. Connect the Ledger to Metamask. Inside the Metamask menu select “Connect Hardware Wallet”.
2. Once connected select the BIP-44 Metamask/trezor path and add accounts.
3. Now the BIP44 addresses will be visible alongside the Ledger Live addresses when you go back to the Metamask accounts page. Now assets can be moved from the Ledger Live address to the BIP44 address.
4. Now go back to Core and access the Core wallet using your Ledger.
5. Add accounts in Core and addresses will show with your newly moved assets.