If you *only* care about single sign-on (and not grade passback), then links from multiple D2L courses that each point to the same WeBWorK course will work for that purpose. It won't matter if you created all those links manually, or if you used the content item selection tool in one course, changed the LMS content ID in the WW course, and then used content item selection in a different D2L course. Or a mix of manual link creation and content item selection link creation.
But grade passback will not work reliably. The way it's all built right now, the WeBWorK course is only "aware" of the most recent LMS course that was used by a user to enter the WW course. If you are under the impression that grade passback has been working with multiple Blackboard courses linking to one WeBWorK course, it's probably a misunderstanding where there are frequent enough logins to the WW course from each of the LMS courses, such that grade passback is eventually getting through for each LMS course. But even then, I would question if the last batches of grades from the last day or so of the term are all getting through to all of the LMS courses.
In theory we could redesign things for this to work. One possibility would be to add things like "lms-course", "lms-course-user", "lms-course-set", and "lms-course-set-user" tables to the database to have all the right things recorded to be used under all the right circumstances. It would include things like sending your (the instructor's) grades to all of the LMS courses you are associated with. But even if that idea is theoretically workable, it would take some work to make it happen.
I use D2L at my school too, and for any situation where it seems like maybe I would want two D2L courses linking to one WW course, I just ask the D2L admins to cross-list the two D2L courses. I end up with one D2L course shell that has two sections of students. I find it much more convenient to only have one D2L course to manage and update as the term progresses. Is that a workable solution for your situation?