Get-SPWebApplication | %{$_.QueryFeatures([Microsoft.SharePoint.SPFeatureScope]::WebApplication,$true)} | %{$_.Upgrade($false)}
Otra opción para un Feature concreto:
$feature = Get-SPFeature -Identity TuFeature $featuresPorActualizar = Get-SPSite -Limit All | %{$_.QueryFeatures($feature.Id,$true)} $featuresPorActualizar | %{$_.Upgrade($false)}