I would consider one of <trike>three four approaches:

1. On each client: Use rsync to upload the file from the client, possibly retrying every five minutes. Rsync can resume transfers that broke instead of starting fresh every time.
2. On the server: Use rsync to download the files from the clients on the server, possibly retrying every five minutes. Rsync can resume transfers that broke instead of starting fresh every time.
3. On the server: Use File::Copy on the server to copy the file from the client using an Admin Share (\\machine\C$\)
4. Push a second Perl executable to the clients that uploads the files. If the client has no network connection, it won't receive the "upload now" command.