With the proviso that I know next-to-nothing about Flash, presumably you can use exactly the same mechanism to communicate locally as you do with a webserver. If your perl program uploads files to the server's filesystem ready to be read by Flash and vice-versa, you can simply write out to local files instead. If you're using sockets to communicate(?!), then the process will be the same as it is already, but replacing the remote port with a local one.

Cheers, Ben.