Based on the fact you mention you're working on Word files and you're calling zip.exe, I'm going to assume that you're on Windows. If so, here's one crazy idea that I'm not will work or not.

Modify the call to run zip.exe to use the DOS command "start", which will launch the command in a new DOS command prompt window. With the zip.exe running in a new window, you can probably use Win32::GuiTest to interact with that command prompt window.

That's probably a crazy, complicated idea, but it just might work. If you do decide to try this and are able to get it work, I'd like to know about. However, I suspect that bulk88's suggestion of using IPC::Open3 would probably be easier to implement.