Not a perl question, but seeing as the monastery has many helpful monks, I can see why you asked.

I don't know the answer, but in short you need to find a way of signalling to an existing emacs process that it needs to load a new file. There is probably a command line option to emacs that tells it to look for an existing emacs process, and then use some sort of private IPC to get the existing process to load the file. The new emacs process will then quit. There might be an alternative binary for the purpose, as there is with GIMP under windows.

In short you need to read the docs, and use google.

Once you figure out the command line, it is a simple matter to invoke it from perl with system

As a side note, does anyone know how to achieve the same with Padre?