When Banktivity does a deep refresh, the aggregator grabs all available transactions from a bank’s website, whereas a regular refresh only gets what’s cached. Since a deep refresh can take a while, Banktivity will sit there waiting for results without showing any indicators. If it is quit before the refresh finishes, it will grab any new transaction the next time it does a regular refresh.

In the new Banktivity (version 8.1.2 or higher), you can force a deep refresh by pressing the Option key on your keyboard while launching the app to get all transactions on the bank’s website and any cached transactions.