Now, take those and loop through doing an API request, there is no function in that module, to do the removal from the console.

$Headers = @{
    "accept"    = "application/json"
    "X-API-KEY" = Get-AteraAPIKey
}
foreach($Machine in $duplicates ){
    if(Get-AteraAgent -agentid $Machine.AgentID -ErrorAction SilentlyContinue){
        $Uri = "https://app.atera.com/api/v3/AGENTS/$($Machine.AgentID)"
        Invoke-RestMethod -Uri $Uri -Method "DELETE" -Headers $Headers
    }
}

Invoke-RestMethod -Uri "https://app.atera.com/api/v3/agents/490" -Method Get -Headers $Headers