Lenore has either trained Sylvia to fight against the Hummingbird Organization or have a back-up escape plan.
Lenore saved Sylvia and was able to hide her during her childhood, but managed to educate her and train her to protect herself. Slightly subverted in Season 2, where Sylvia was sent around the world by Lenore to hide from a man named Daniel Rassmueller, she met him and was almost killed by him, but is still fleeing nonetheless. A lot of the Hummingbird Organization's tactics has involved gaslighting.
We never really see or hear any proof beyond what is seen and heard. We know that the reverend was killed by a drunk driver, but we don't have any other details. Maybe the driver really was drunk, was paid or was simply set up. Same with the guy who banged his head on a door and said "this is your first warning" and then disappeared leaving behind enough blood to indicate that he bled out. He could've just been putting on an act and the blood could've been stored beforehand. The tech has two major drawbacks: you can't use it on someone without the tech and you have to take supplements in order for the thing to work properly. Ultimately, their end-goal was to get Lia's uncle to come out of hiding since they still want him for some reason. Everything they did was to manipulate Lia into continuing the investigation and keep her so scared that she wouldn't have time to think. Same with the survivors. If they wanted to stop Lia, they'd do it before she could ever even start.