The lights being on are what bother me the most. I don;t know why an intruder would turn them on if he knew people were sleeping in the house, but I don't know why the father would point out they were on when he came home if the parents had anything to do with it. That's not something you would put in a 'story' about an abduction. I also don't see the mother running in to jump in bed when dad drives up and not having time to shut off the lights. Why would they be on unless she was cleaning up evidence? If she was still cleaning up evidence then LE would have found evidence of midnight cleaning.
The phones I get. We leave ours all over, on counters, night stands, charging and not charging, whatever...reprogramming numbers is something we did this week twice. Hubby dropped his in a bucket of oil at work. We have a spare and had to transfer numbers etc to the spare phone and then yesterday we replaced it with a good data phone and transferred stuff all over again. It happens.
I can also see the 6 year old getting up in the night and heading for mom and dad's bed...all of mine have done that when they had nightmares or gotten sick and they don't necessarily wake me up when they come to snuggle.
So all that said the only theory of the lights being on that works for me is if the 6 year old turned them on as he headed from his room to mom's...which would be unusual to dad because it was the first night he came home to all the lights on...being it was his first night at work.