if ( $ftp->delete ( "$Target/$FileName" ) ) {
   print "File <$Target/$FileName> was deleted\n";
   } else {
   print "File <$Target/$FileName> failed to delete\n";
}
[download]

I asked:

Does deleting a file with a dot at the start of the name work from the command line ftp client?

I take this as you trying to address this:

I can delete from bash on the server.

This is not what I meant. I meant using a remote machine, using another ftp client.

If you cannot delete the file using any other FTP client via the ftp server, then the problem is not with Net::FTP but most likely with the ftp server.

If the Windows default client does not support passive mode, then maybe you can check using curl or wget, or some other approach with a client separate from Net::FTP.