Recently I implemented Azure Arc in a production deployment. After seeing that it's working perfectly outside a POC/Demo environment, I decide
I will keep this post as short as possible.
If you're managing your servers with Azure Arc then be wary that by having the default Guest Configuration policy enabled, it will setup a PowerShell DSC configuration which might break your SQL Servers.
If you're managing SQL Server instances with Azure Arc and for some reason your Replace Process Level Token policy gets overwritten and your SQL Agents are crashing then just remove the Guest Configuration from the Server
The policy by default will overwrite the Process Level Token permissions and remove the SQL Server agent from there thus breaking jobs and other things that your devs run :)
So if you're having issues that every 15 minutes a configuration gets reset and your servers are managed with Azure Arc then check if your servers has a DSC configuration installed and then validate the guest configuration policy.
Hope this helps.
Have a good one!