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.

Hi,
The "false" transaction appears in the Ledger Live as well, even with "Extended account search" (what does this even do precisely ? what derivation paths does it look into ?) and Custom gap limit = 999 ...
Additionally, I generated about 50m addresses from my mnemonic with the most used derivation paths and variable ranges where I thought the coins might be, but didn't manage to find this address ...
I honestly looked a lot into this and I couldn't find anything similar to this described over the internet (well, at least not recently) so I think that the conditions needed to replicate this bug/exploit are very specific, I wouldn't worry about it too much if i was you ... (hell, if you manage to replicate this, you can claim a bounty with Ledger which in most cases will be bigger than the lost amount ...).
When sending the remaining coins to a custodian afterwards, I restored my wallet from the seed to a new Ledger device and used the new one to sign on an offline machine the last transaction which went through properly, so I guess you can do this if you're worried ...