Hi @Boricua,
I think I can address most of your questions...
First about the combining (cross-listing) of sections and enrollment changes... It will depend a bit on how your school handles the enrollments, specifically whether the "old" enrollment becomes deleted or marked as inactive. If it's marked inactive, you could possibly run into a few glitches, as one section would be inactive and one would be active, but I think Instructure has addressed a lot of those little glitched in the last year so hopefully it won't be bad. If the "old" enrollments are marked as deleted, you shouldn't run into any issues that I know of in general.
Around when you do the cross-listing and whether both courses should be empty... You don't have to have both course shells empty to do the combination (but you probably do want to have one empty, as content is not merged together). One thing that trips people up often though is that to do the cross-listing, you'd want to start from the empty course shell and cross-list that into the course shell where you've done your development. I always recommend doing the cross-listing before students are able to see the courses, just to avoid confusion. In a case where you do have content in both course shells, it's critical that you do the cross-listing before students do any work (assignments, quizzes, discussions, etc) since no content or submissions is merged when cross-listing, you'd completely lost access to all of the already submitted work.
For your final question, students will all see the title of the combined course shell on their dashboard. This can be confusing to the students who are registered in one of the other courses that have been combined in Canvas, so I recommend making an announcement or sending a message to all students letting them know about the combination and that Canvas may show a different course title than what they registered.
Hope this helps! Let us know if you have more questions or any followup!
-Chris