He's having trouble remembering to put his completed homework in his folder? And that his binder/folder is overflowing? Are those the core issues? When he has the homework in his folder, does he remember to turn it in in class?
If so, I recommend that you work with him to ensure that his homework is in his folder every evening and that his folder is in his backpack, ready to go in the morning. It may take many repetitions of you reminding him, but eventually he will remember on his own.
As for the binder, when you have an hour or two to spare, work with him to organize his binder and get him a second one if you have to. Then once a week have him transfer the papers that have been graded (or are no longer in play) from the folder to the binder. This will take a lot of executive functioning on your part to ensure that this is done, but you are modeling what it takes to stay organized over time for him. Eventually, he will be able to do this on his own.
By the way, when I say "eventually," the time scale I'm referring to is in years, not days or weeks.
That said, the teacher's behavior about forgotten homework is unprofessional (at best).
