I had a problem with missing transaction on Ledger app,but it was because I use one of the address from Sign Message option which is not visible to Ledger Bitcoin App,but it was still there and with increase gap address limit in Electrum problem is solved.
It is not possible that address is just disappear like it was never part of that seed...
OP it would be good to post that transaction and photo you take with that specific address.
this is a known issue with ledger nano
check this:
https://www.reddit.com/r/ledgerwallet/comments/6yi161/signing_a_segwit_address_message/?st=jc1mwoja&sh=7589a31eWhen you sign a message with a segwit address in ledger nano, it will sign a message with the associated legacy address, as there is no standard to sign with Segwit addresses yet.