Safest bet is to call FinCEN and/or your regulator. Everything else is just guess work from the peanut gallery (myself included!).
I would mark Unknown (it's not technically wrong!). Then I would update my CTR policy and procedures and note how we handle these accounts and do the same for all of them going forward.
My two cents: Even if FinCEN/regulator were to find this one CTR, it hardly shows a systemic failure of BSA and would not warrant a finding.
I think I would file it and move it to the next big issue.
If you do happen to call FinCEN or your regulator, please update us! I'd love to hear their thoughts.