Have you tried creating a wallet account on Ledger Live to see if the BTC shows up as missing there too? If it's an Electrum bug, it must show up in Ledger Live. I think Magnum Wallet (no need to download it) works as well with the Bitcoin wallet on your Nano S. Suggesting this in order to see whether it's Electrum's fault or there's a serious security risk with the hardware wallet. If the latter is the case, then I gotta put mine away for the time being.