Course A doesn't know that the content in course B is the same. It doesn't look at names and say "These are both called syllabus quiz so they must be the same document and I should replace, rather than copy." Things in Canvas are based off of IDs and even if course A and B were both created from the same import (you copied both from the same course to start with), they have different IDs once they are in course A and B.
To verify this, I went into our test instance of Canvas (beta was down) and took a course and copied it to another course two times, appending an A or B to tell them apart. I then went into the A course and deleted my entire chapter 4 modules. In course A, I told it to import the chapter 4 module from course B.
After the import, I did have the chapter 4 module ... at the end of the modules page, but all of the content pages inside of it were duplicated and had a -2 at the end to represent that it was the second copy of the item. The discussions and assignments (I didn't have any quizzes in that module) kept the same name.
However, when I went to the discussions page, I had two copies of the discussion with identical names. When I went to the assignments page, I had duplicate copies of the assignments with the same name. The original from course A was in the assignment group where it had started, all of the imported content was in the "Imported Assignments" assignment group. If you're not careful, you could easily delete the wrong assignment, so I would delete things from the other assignment groups and then move the item from Imported Assignments, rather than moving the new ones next into the proper assignment group and then deleting the old ones.
What you're talking about is actually a hack that has been used for a while to duplicate classic quizzes. There is no direct functionality for copying a quiz, but you can import the content into the course (there may be some issues with importing it more than once).
What you would need to do is delete all of the old assignments as well as deleting the module before you do try the import. If any students have already submitted things, then stop. Deleting the assignments will cause students to lose their submissions.
You should probably delete the content pages before you try the import as well. Then it wouldn't duplicate the names because the originals were gone. If you don't delete them and import, then renaming after the fact is time consuming. You would need to go to the Pages listing and delete the page for each of the items that was duplicated and then rename all of the content pages to be the name without the -2 at the end.
You will also need to go back and move any assignments into the correct assignment groups.
If you're going to do this, it's just simpler if you delete the modules and the content in the modules first (hopefully no assignments are used in multiple modules) and then do the import.
We encourage our faculty to develop their courses in a sandbox and then copy them into their actual courses. You may be able to do a course reset and then import all of the content from course B into course A, treating course B like it was the sandbox course. Don't do that without talking to your local Canvas Admin first, though. They would break things on our student information system's end if they did that since it caches and relies on the Canvas course IDs remaining constant and that changes when you do a reset.
