We are a large Community College with very few, if any, traditional cross listed courses, so you can take my answer for what it's worth. We also use the 1-to-1 model for all of our courses and sections, with everything populated via SIS.
How I manage it here is that any instructor who is teaching two or more sections of the same course can submit a request for their sections to be merged in Canvas. They can submit their requests to me at any time, but I will only perform the merge in Canvas during the week prior to the first day of classes. I do this specifically to avoid the issue of sections being re-assigned to someone else, like you mentioned. I also warn them to not load any content into the shells in Canvas until the merge is completed, since content will not carry over with the merge. I will not perform any merges after classes have started, to avoid any possible risk of student data being lost in the process. As far as I know, the course(s) being Published/Unpublished doesn't matter much.
When I perform the merge, the only names/IDs that I change are the Name and Course Code fields of the "new" merged shell. Here's an example:
Course 1 Name: CHM1046 (160367) - General Chemistry II
Course 1 Course Code: CHM1046 (160367)
Course 2 Name: CHM1046 (160368) - General Chemistry II
Course 2 Course Code: CHM1046 (160368)
---- Post Merge:
Course 1 Name: CHM1046 (160367 & 160368) - General Chemistry II
Course 1 Course Code: CHM1046 (160367 & 160368)
If I merge more than two sections together, I rename them like this: CHM1046 (160367, 160368, 160369) - Gen Chem II.
All SIS IDs are left in tact, including all Section information. As procedure, I always roll the higher reference number into the lower one, so I went into 160368 in the above example and merged it into 160367. It really doesn't matter, it's just what I always do.
I do this process manually, and only by request. We've only been on Canvas exclusively for about 1.5 yrs, so right now there are only about 5-6 requests each semester that I have to process. Since it doesn't take much time, I have not looked into automating the process at all and do it strictly manually.
Hope that helps!