The school has a few devices that no longer reports back to Meraki SM, because
This device is using an outdated APNS topic and needs to be re-enrolled. Unenroll the device, and then enroll it by following the instructions on theiOS deployment page.
I went to the Settings >> General >> Device Management on the device, I can see Meraki Management, but there is no Remove option. I believe the Meraki SM Agent was pushed to the device via Apple Configurator 2 / DEP.
The profile restriction also disabled Safari, App store.
I'm now in this situation where I can't remove Meraki management on the device (Remove option not available) and I can't perform Selective Wipe / Erase Device from Meraki Web console as the device is not communicating back to Meraki.
I have Apple devices that no longer talk to system manager as well. My only fix was to use the Apple Configurator 2 and prep each device like it was new. After performing this action and without deleting it from Meraki, System Manager was able to communicate with the device. Then all app that were assigned through my profiles were reinstalled as well. Hope this gives you some light at the end of the tunnel.
When I connect the devices to Apple Configurator 2 I get
Paring is prohibited by policy on "iPad"
The supervision configuration for these devices does not allow pairing without the supervision certificate. Create an organization with the correct supervision identity, or re-supervise these devices with paring allowed.