Some of the transactions on our store got flagged as "hidden" for some reason (and we don't think it was our staff that did that), and we're trying to track down why that might have happened. But that aside:
For anyone else who finds themselves in that position, and are wondering how to get them to be NOT hidden anymore, the trick is that the "Hide Checked Transactions" button is mis-labeled when you're viewing hidden transactions. What that button label should really say is something more like "Save Changes to 'Hide' Status" - meaning that if you have hidden transactions, you would uncheck the "Hide" checkbox and then click the "Hide Checked Transactions" button to unhide them.
I wasn't able to find information or an answer about this flag anywhere else, so I'm posting it here in case it helped others