That’s a lot of questions! I’ll just answer a couple:
(Question 5) Don’t change the files on the sync target directly (ie. on OneDrive). Yes it can make Joplin go crazy. There is no option in Joplin to remove duplicate notes unfortunately
(Question 16) As your note collection is small, it’s probably best if you do a full reset. Some details for how to do that are here How to fix synchronisation issues and start over