There's nothing I know of in the Jamf console that lets you pause or change the check-in for a single machine, or even multiple ones. It's a global setting that applies to all managed machines.
What you could possibly do is send a command to the single machine to disable the Jamf LaunchDaemon that controls the check-in. I'm not sure if there's something in the Jamf framework that "fixes" a disabled LaunchDaemon or not though. I know there are a few items the Jamf agent will fix, but the actual check-in daemon may not be one of them.
