When it comes to the scene in the second movie where Emmet is running up the staircase to crash the wedding, a lot of the time people focus on the part where Emmet says 'The real Lucy would never say that'.
AND YEAH. It is a really sad line, but I think one of the more important ones was when Lucy was telling Emmet about how she used to like Everything is Awesome, and Emmet responds with
'No, no, you would've told me!'
I think that line hits the hardest because you can hear the distress that is in his voice. He is genuinely surprised and unable to handle the sudden change in his worldview, because he spent 5 years having Lucy tell him, and even reinforce the fact that she was a tough rebel and nothing else.
So for her to go up to him at a time of extreme urgency, and proceed to tear all of his beliefs about who she was down? It's no wonder Emmet didn't believe her.
Emmet probably got some trust issues from this experience too. Another reason he said 'you would've told me' was because he trusted Lucy. He trusted her with his own emotions, and past, and probably his secrets too. So the idea someone he trusted so much was lying to him the whole time? It was easier to believe she was just brainwashed than lying about everything about herself to him.