I noticed that after the Thanksgiving episode and the epi where Chet got a job as a janitor, Verna disappeared. I thought they were happy. How come she left again?

she was mentioned again in season 7 in episode family tree

There were a couple of times in season 6 that she was referred to by both Shawn and Chet as "wherever the hell she is" but exactly when or why she left was never explained.