I had similar but in a very simple cloud software, years ago, the client had deleted 3 customers and all the related transactions in an effort to "archive them"..... #painful. Undid 18months of bank rec's... Shouldn't be possible in the same way in NS though.
In case it helps, a few thoughts that come to my mind of where I'd look. 🙂
Ask someone to re-reconcile the account, or export and compare with the bank, can they see the issue/what's missing/what's unticked? If you've got a variance, hopefully something should stick out & it'll give you a transaction to look at and start with.
Audit trail for changed or deleted transactions that would be linked to that bank account and is within the time frame. Is there a lot of them/a particular user that's doing lots of edits/changes/deletions?
Were the accounts locked or closed? It might be worth looking to get the accounts locked & closed earlier to ensure no one can go back and change transactions.
Which roles have permissions to edit payments, who has them, focus on them in the audit trail?