Introduce a 'Force Check In' button
Add a button to force all devices to check in. If a device cannot check in after this, then flag it.
This will help identify issues with the installed profile or check in issues.
A "Refresh Inventory" command should do this already. If a device is still not responding (eg. updating the "Last Seen" time), that means there is something preventing the device from receiving MDM commands and/or responding to the MDM server. Apple's MDM protocol does not currently provide a more forceful option, nor is there a way for an MDM to reliably diagnose the reason for a device's inability to respond to a command. For example, if it is a network issue and something is blocking the commands, MDM does not currently get any feedback in order to know the command was blocked by the network.
As it stands, SimpleMDM automatically sends a refresh command to devices hourly. Admins can configure notifications to be sent to them if a device has not checked in for X amount of time.