How to overwrite documents that require check out?

you have to fist check out file

foreach ($file in $files) {
    $file.CheckOut()
    $stream = $file.OpenRead()
    $done = $list.RootFolder.SubFolders["Hertel"].Files.Add($file.Name, $stream, $true)
    Write-Host $done.Name "Uploaded" -BackgroundColor Green
}