Blackboard has a nice feature to automatically manages multiple sections of the same course. A system administrator will have to set one (or more) of your courses as child courses of a parent course. Then, in the parent course, you’ll be able to see which course students are actually enrolled in and our automatic enrollment integration won’t be affected.
Just let us know (login required) which course you’d like to use as the parent and which course(s) to link as child. It’s best if you haven’t created any content or had any interactions in the child course(s) before merging.