Thank you for
reaching out on the community and telling us about your issue. That is odd that not all of them come through. We could try deactivating and reactivating to see if we're able to refresh the connection to download consistently.
I would recommend first saving a backup so that we're able to go back just in case.
Next we'll deactivate and reactivate the accounts. The steps to do so can be found in the articles below.
Once we're done ideally we should be getting those transactions that didn't come in the first time. Try it out and let us know if that's the case and if not we'll see what the next best step is.