Hello Graci,
another idea I would take a look at is to use a "general purpose" executable, that makes use of Dynamic VI calling. With this approach, your exe would be fixed (you never recompile it), but it calls dynamically the vis you tell it to (and those are the ones you modify/update). Have you seen the VI Server Plug-in example? That's a good example of a plug-in architecture that may solve your needs.
Regards,
JorgeM.