[Molchune]

Как то так

Код:

$source = "C:\tmp\source"
$target= "C:\tmp\target"
dir $source -Directory | %{

$folder = $_.Name
Test-Path $target\$folder

If (Test-Path $target\$folder) {
    $i = 0
    While (Test-Path -Path  $target\$folder) {
        $i += 1
        $folder=$folder.Split(".")[0] + "." + ($i | %{"$_".padleft(3,'0')})
		}
	}

 Else {
    Copy-Item -Path $_.FullName -Recurse -Destination $target\$folder #-Force -Whatif
	}
Copy-Item -Path $_.FullName -Recurse -Destination $target\$folder #-Force -Whatif
}