You're right they wouldn't know. But they aren't trying to make the EM wave change. They're trying to create and expand the world wide system that utilizes the EM waves the Geo tells us about in the beginning of the game. Situations and circumstances during the activation of said system, or machine at this early stage, would cause our (The player's) Navis to react and change in a way. Stumbling onto the actual EM Wave change would be a mere coincidence. And even if it was not we could always introduce an AMian and/or FMian to help establish it for our characters. Even then the scientists might not know or even find out. 

Even if their are loose ends and point you could nit pick I'm sure I (or we) could come up with something to allow the story to work and progress. Ya know? Megaman as a whole has a history of making certain things a bit plot hole ridden and ambiguous. Which allowed them to tell the story they wanted while giving employers and fans what they wanted. I may or may not have been studying up a bit and watching youtube videos to help with planning... XD

EDIT: I also fear you may be forgetting that EM Waves aren't simply what allow the transformations. They are simply the Electromagnetic waves that surround the earth. The scientists would be using them to convert from the basic and older Network system to a newer system with larger capabilities and such. [url=http://megaman.wikia.com/wiki/EM_Wave]They're more important than just allowing a human to undergo EM Wave Change. That is just one thing that can be done and one part of a the hole that most humans in the serious for a time didn't even know about. It's possible the scientists could be trying to make one thing and accidentally create another throughout their success. Even without knowing they made an "extra discovery".