<p>At the moment, i think Lucas killed Charlotte to protect Hanna, worried that Charlotte would become A again. It makes sense since upon being asked by Hanna if he was in Rosewood the night she was killed, he not only looked worried that Hanna had found him out but also he didn't even answer the question. He even  immediately agreed to be Hanna's alibi since if the police ever suspected him of being the killer, he already has an alibi in place. </p><p>If Lucas really is the killer we can assume that in Season 7 when they are given 24 hours to find Charlotte's killer, they turn over evidence of it being Lucas (either that or Lucas finds out what happened to Hanna and comes forward) but then A kills him and keeps Hanna hostage if they don't take care of the body, leaving them no choice but to burry his body where no one will ever find it. This is the mistake that Marlene talked about that A will use to fuel the endgame. </p><p>Furthermore, it has been a five year time jump and they could have instantly brought back some main characters like Jenna, Jason, Wren, etc. but no, they bring back Lucas in the first few eps of 6B. Marlene wants to make sure people know that he is still around and maintains a connection to Rosewood. </p><p>I am most likely to be 100% wrong but it is fun to theorise :) </p>