Charlotte, sounds to me like it is he doesn't want to leave his brother behind. Do they have mixed playtimes - supported learning and the rest of the school? Maybe worth explaining that they can still play together at intervals etc - and that way they will have lots to tell each other when they meet up again
Have they spent much time apart - that may be a factor as well if not, hence why Thomas reluctant to move, and Adam just picking up on his brothers anxieties or worried himself cos they will be apart.
Def speak to them both, and the teacher at parents night. Do they do annual reviews about the needs of the children - if so have you had theirs yet. If not bring it up at the review as well, other specialists involved may have other ideas.
Another wee idea - ask the teacher about the possibilities of Social stories. These are simple stories that can explain what is happening to the child. So one for Thomas would be about moving out of supported learning, and one for Adam about being apart from his brother. They were initially designed for children with Autism, but are becoming much more commonly used with all children with learning disorders of all kinds. They really work - have a wee hunt on google for them - fairly easy to write yourself if no-one else can help. Carol Gray was original author.
Keep the timetable etc at home, and bedtime back to normal, and hopefully it will all settle down again soon