I'm confused by your description. I understand that you have two perl apps that run independently -- Do they both have GUIs? Your opening sentence also mentions a "compiled exe" (so I gather you are using ms-windows) -- How does this relate to the two perl apps? Do you generally (or sometimes) use each app independently, or are they always used in combination (because they are interrelated / interdependent)?
Here's a suggestion, based on a wild guess about what you are trying to describe. If app2 will continue to be useful on its own as a GUI, and a particular subroutine in app2 does what is needed in app1, then the simplest thing would be to isolate that subroutine as a module (along with anything else it needs to do its job), so that both app1 and app2 can use it, without getting bogged down in IPC issues (which tend to be a little trickier when applied to scripts that have GUIs).
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