The problem with many of these threads is that no concrete feedback can be given without having seen the script. The evolution of this thread from 'rap' to a stolen device by one of the two inventors to now becoming a janitor stealing a device from two guys with opposing motives is a slippery slope. As a group we can collectively brainstorm but without the actual script to respond to, it's our imaginations.
Inarius and others have interesting concepts that are never fully presented. So no matter what suggestions are offered, they offer a "yes but". Not to be argumentative but because they haven't disclosed enough for anyone to realistically help them.
Inarius, in solving your plot hole, you need to put yourself in the place of your characters and be real. Let's say you and a friend write a script. You want credit for writing it and a portion of the sales. Your friend, unknown to you, already has a producer ready to make this but doesn't want to share the money. The producer is willing to help your friend rewrite the script so they can split the difference. In the meantime, a friend is sleeping over and reads your draft. She likes it, takes it and puts her own name on it with a few key changes and shows it to a producer she knows. Her project is successfully funded through Kickstarter. Unfortunately, one of the crew for her producer is good friends with your co-writer's producer. Would your co-writer decide to sabotage her project long enough that he and his friend can finish their version? Would you be content with either of them making it as long as you got credit, though not the money?
I believe that captures the elements you presented. How would you really respond? That's what will make your movie feel real and believable. Hell if it's a prototype and only the bad guy knows what else it's capable, he can still call the police. Unless I tell you it's a time machine, all you know is someone stole a wristwatch. Even if the thief says what it is, he's still in the wrong. The 'hero', villain and audience know, but no one in your fictional world knows. In the scenario above, no one on this forum knows what your story is about in any detail. However any co-writer and visitor to your home who reads it would.
While there has been lots of talk about legal aspects, for me it's a fundamental question of believable response by your characters. Neither inventor has anything to lose by reporting the missing device. Even if the janitor did steal, they build a new one. Just as you'd write a new script. It could be the janitor stole it only to alter his voice not realizing that it also allowed encoding voice frequencies that influenced people's minds. Maybe only the villain knows. And depending on how desperate/evil the guy is, he may kill off his partner if s/he also realizes its other use. There are many ways to play this gambit.
You have to be careful as a writer not to force fit behaviors just to make the situation you want result in the end. Natural consequences of believable choices make for more interesting drama. Consequences of unbelievable choices makes for comedy. Is your co-writer going to gun the car and run over the girl just to protect his interest. Or even just death threats? Are you going to sue your friend when he and his producer buddy make their film without crediting you? How much legal expense are you willing to put into the lawsuit against your friend if you know you'll probably pay more than you'll receive. How much is that writing credit worth?
As an exercise, I'll often provide students with a dilemma and ask them to generate five different responses and let them play out. It's sometimes good because it can free your story to explore different ways of getting to the same end. Same is true of acting out a scene using different motivations for responding.
I don't know how your story goes. But if, as a writer and/or actor, it feels wrong to you, then the problem is the choices are forced and not natural. You need to go back work forward from normal choices. If something is stolen, it gets reported. However, knowing the police, not every department gives a damn. They may send someone out to get a report and then it gets filed and nothing ever comes from it. I sense that your block may be that you think reporting the theft will generate a manhunt. That is seldom the case. In a case I heard about, the visiting police officer didn't even dust for prints after the break in. If this was a garage lab, the police are less like to be interested than an industrial research lab. Even a university theft will probably generate only a momentary blip of activity. Things are stolen all the time on college campuses. Police involvement doesn't bring out the CSI and dogs unless there is suspicion of a major crime. And your two inventors may downplay the theft for their own reasons.
All I can suggest is that you write natural logical responses to unusual circumstances and it will make the situations flow better.
