I normally don't like to launch a feature that's this rough around the edges, but I decided to anyway. I added a section to the OwnYourSwarm dashboard that will let you import a specific checkin by its Foursquare checkin ID.
When you click "Import", the processing flow for that checkin is started in the background. There is unfortunately no feedback in the UI on its progress yet, but in a couple of seconds you should see the checkin appear at your website. Shortly after, any coins, likes, and comments are sent via Webmention as well.
In the mean time, you can at least enter a checkin ID manually to trigger an import if any were missed because they were "offline" checkins.