The more Luke's soul fragmented due to the curse, the stronger the bond between him and the spirit of the Scales harbored within his body became.
And what was previously only possible when Luke was unconscious, was now possible when he was awake. Communication between the two became faster and easier, which certainly helped Scales when she needed to pass on directions, but it fatigued Luke even more.
Several times a day, Luke would cough up blood and stay up nights because of a lacerating headache. He tried to hide this from Meredith, but she was smart and could tell.
Even though she noticed everything that was happening to her best friend, Meredith didn't stop him from continuing his journey, deciding for a while to just stay by his side. However, when they arrived in Stahurt, Luke's coughs became even more frequent and she decided that she couldn't keep quiet any longer.