I would have to agree on Lulu's points on this; well said, Lulu.
I doubt, other than limited personal experiences, that any pokemon with a normal IQ, like your flygon, would have little to no understanding of the virus. In order for it to understand any immunities or resistances, it would need to have studied hundreds, thousands of specimen going through the entire lifespan of the infection. I would be able to see, though, that maybe instinctual knowledge, like "This pokemon was infected, therefore, it might be in its meat-- I shouldn't eat that," or "This water has infected blood in it-- I shouldn't drink that," or maybe even "That pokemon's infected, I shouldn't let him bite/wound/lick me because it might get me sick too." It would be all right to play into natural instincts to avoid the sick, but a different thing entirely to actually know what the virus was doing, if that makes sense.
And, as Lulu pointed out, unless the flygon has been working with technology for a long time as a flygon, there's little chance that would be allowed. Trapinch and Vibrava are not the best choices when it comes to using and understanding human tech, and therefore might only be able to understand a very limited amount of the tech at hand, as she suggested, like pressing the button= picture on the screen. Your character wouldn't have been able to successfully handle it until they evolved into their final evolution, which, would require a lot of out-of-the-lab training anyway. Level 45 would be hard to get to in a lab full of cameras, so I find it hard to believe that a trapinch/vibrava would be able to learn anything while struggling to level up.
And no, no battery would last two years without a charge, so any tech would be completely useless anyway.