Electrum_LedgerNS_Issue, is there any new information regarding your case? I see that the problematic transaction is still intact/unspent which can be a good sign (if it is not in the classical hack), which means that there is still hope for a solution.

I have something similar in past when I play with change address from Ledger, and one transaction was invisible because Ledger Chrome app was set to not check all addresses. I fix that in Electrum with increasing the gap limit. If only the solution would be so easy in your case...