THE SOLUTION. It was all about a matter of REGEX, I had select all <!--START--> <!--FINNISH--> tags that also contains <tr> </tr> tags, so as to parse only their content
$sourceFiles = Get-ChildItem 'c:\Folder1'
$destinationFolder = 'c:\Folder2'
foreach ($file in $sourceFiles) {
$sourceContent = Get-Content $file.FullName -Raw
$contentToInsert = [regex]::match($sourceContent,"<!--START-->(\s*)<tr>[\s\S]+</tr>(\s*)<!--FINNISH-->").value
$destinationContent = Get-Content $destinationFolder\$($file.Name) -Raw
$destinationContent = $destinationContent -replace '<!--START-->(\s*)<tr>[\s\S]+</tr>(\s*)<!--FINNISH-->',$contentToInsert
Set-Content -Path $destinationFolder\$($file.Name) -Value $destinationContent -Encoding UTF8
} #end foreach file