@AK The missing transactions are actually not present in the BAI2 files at all. I know when we used Bank Feeds, data would be imported on a rolling 7 day basis. I've tried to get our bank to do this, but they seem unable or just aren't sure how to do it.
To your point, the transaction codes actually were the first thing our bank suggested may be the issue, but I sent them a list of natively supported transaction codes that I found in the help section. They've told me that they've mapped their transactions to that format. But the fact that the transactions aren't included in the file at all makes me think that it's a separate issue entirely.