The Issue

$WorkspaceID = 'xxxxx-da5f-yyyy-bfbf-zzzzzzzzzz'
$WorkspaceKey = 'YourWorkspaceSuperSecretKey'
$PastDays = 3 #How aggressive to clean up

#region Remove Hybrid Worker from Azure
if ((Get-Command Get-AzureRmAutomationHybridWorkerGroup).Version.Major -le 5) {
    Write-Host "Please Update AzureRM.Automation module by running : 'Update-Module azurerm.automation -force' as Administrator"
} else {
    Connect-AzureRmAccount
    Get-AzureRmSubscription | Out-GridView -passthru | Select-AzureRmSubscription
    $ResourceGroupName = Get-AzureRmResourceGroup | Out-GridView -PassThru | Select-Object -ExpandProperty ResourceGroupName
    $AutomationAccountName = Get-AzureRmAutomationAccount | Out-GridView -PassThru | Select-Object -ExpandProperty AutomationAccountName
    $date = (Get-Date).adddays(-$PastDays)
    $workers = Get-AzureRmAutomationHybridWorkerGroup -ResourceGroupName $ResourceGroupName -AutomationAccountName $AutomationAccountName 
    $workers | where-object {$PSItem.RunbookWorker.LastSeenDateTime -le $date} | foreach-object {
        Write-Host "Processing {$($PSItem.RunbookWorker.Name)}"
        $PSItem | Remove-AzureRmAutomationHybridWorkerGroup 
    }
}
#endregion

$servers = (($workers | where-object {$PSItem.RunbookWorker.LastSeenDateTime -le $date}).RunbookWorker).Name

#region Reload configuration and report back
Invoke-Command -ComputerName $servers -ErrorAction SilentlyContinue -ScriptBlock {
    $WorkspaceID=$USING:WorkspaceID
    $WorkspaceKey = $USING:WorkspaceKey

    #Create COM Object to manipulate MMA configuration
    $AgentCfg = New-Object -ComObject AgentConfigManager.MgmtSvcCfg
    # Remove desired OMS Workspace
    if($AgentCfg.GetCloudWorkspace($WorkspaceID)) {
        $AgentCfg.RemoveCloudWorkspace($WorkspaceID)
    }

    Stop-Service -ServiceName 'HealthService'
    Start-Sleep -Seconds 3
    #Remove files
    Remove-item -path 'C:\Program Files\Microsoft Monitoring Agent\Agent\Health Service State' -Force -confirm:$false -Recurse
    #Remove registry
    Get-ChildItem 'HKLM:\software\microsoft\hybridrunbookworker' | Remove-Item -Force -confirm:$false -Recurse -ErrorAction SilentlyContinue
    #let it rest a while. It was a hard task! :)
    Start-sleep -Seconds 5
    Start-Service -ServiceName 'HealthService'
    Start-Sleep -Seconds 3
    # Add OMS Workspace
    $AgentCfg.AddCloudWorkspace($WorkspaceID,$WorkspaceKey)
    $AgentCfg.ReloadConfiguration()
    Start-Sleep -seconds 3

    $AgentStatus = $AgentCfg.GetCloudWorkspaces() | select-object WorkspaceID,ConnectionStatus,ConnectionStatusText
    $ServiceStatus = Get-Service 'HealthService' | select-object Status,Name
    $HybridWorkerRegister = Get-ChildItem 'HKLM:\software\microsoft\hybridrunbookworker'
    [pscustomobject]@{
        ComputerName = $env:ComputerName
        AgentWorkspaceID = $AgentStatus.WorkspaceID
        AgentConnectionStatus = $AgentStatus.ConnectionStatus
        AgentConnectionStatusText = $AgentStatus.ConnectionStatusText
        ServiceName = $ServiceStatus.Name
        ServiceStatus = $ServiceStatus.Status
        HybridWorkerName = $HybridWorkerRegister.Name
    }
}
#endregion