How to force Windows Agent to check in with SophosCentral

What does "C:\ProgramData\Sophos\Management Communications System\Endpoint\Logs\MCSClient.log" have in it?

Is it sufficient to restart the Sophos MCS Client service?
You will need to disable Tamper Protection to do this.
You might have to run 
SedCcli.exe -tpoff <pass>
to do it if MCS is not working at all.

In addition to this, were there any recent changes on your network set-up recently. this will also cause communication issues. to further check, you may send the logs with us. 

Hi, so these machines are remote. The policy seems to state for them to check in with the Sophos cache server that is on site at 4am. We know with high degree of confidence that the machines are not on VPN at 4am as of the pendamic. So they can not reach the cache server. Does the agent check in on a cycle or maybe looks to sophos in the cloud when it can not reach the cache server?

Yes, you are right about it. If Updating through the Cache server fails the endpoint will automatically redirect it to updating through the internet. Provided that the network where the machine is connected has open access to Sophos domains and ports or either it uses open internet then the endpoint should be able to communicate to central. 
Can you share with us the logs from those machines which is failing? 

Hi, so these machines are remote. The policy seems to state for them to check in with the Sophos cache server that is on site at 4am. We know with high degree of confidence that the machines are not on VPN at 4am as of the pendamic. So they can not reach the cache server. Does the agent check in on a cycle or maybe looks to sophos in the cloud when it can not reach the cache server?

It would be better if you can share the MCS logs which can be found on C:\ProgramData\Sophos\Management Communications System\Endpoint\Logs\MCSClient.log.