Client's aren't checking in after long uptime.

Are you getting any kind of feedback in /var/log/jamf.log?

Have you done a recon while ssh'd into one of the systems to see what the result is. Also, try sudo jamf policy -trigger every15

What determines if a Mac checks in isn't so much whether the JSS is available as much as if the daemon that controls the scheduled check in is running.
While it really should be, you may want to also do the following when ssh'd into one of the affected Macs

sudo launchctl list | grep jamf

See if an entry for something like com.jamfsoftware.task.Every 15 Minutes shows up. It should be there. If it isn't then the daemon isn't loaded correctly, which is rare. More likely would be that it has an exit status of something other than 0 if there was an issue.
But there could be other reasons as well. Check to see if the jamf binary is in the middle of a task, like inventory scanning. We've seen it occasionally get stuck on something and seemingly never exit.