We have been battling this since Day 1. After working with Jamf a few times on this my only solutions are to
1 - repush the app
and if that alone does not work
2 - completely remove the device from the process by deleting it from the Profile - uninstalling the app - then adding it back
I have several devices that I have had to do this multiple times
So far the new version seems to be working as expected. I still have a few that stopped checking in before summer and now trying to work through those. A few just took a restart. One I had to uninstall Protect, remove from config, add back to config, redeploy pkg for it to check in again. Will see how it behaves going forward.