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...
This might be the solution here, one can only hope.
It's disturbing because it seems like this points to a bug with either the Ledger or Electrum. I don't see anything the OP could have done to cause it, so it's probably not an operator error. I use a different hardware wallet myself, but I use Electrum, and own a Ledger. If this an issue with Electrum it may not be limited to one brand of hardware wallet, which is quite concerning.