While it’s not incorrect to only use the Global Inbox, its intended purpose is to temporarily hold transient or unfiled documents. Think of it in the same way as its real-world, analog… analogue 
Imagine if you tried to use the Inbox on your desk at work as your filing cabinet.
Are you referring to imported or indexed documents?
I think that when the note is moved back to the inbox, it should be a replicant again, not the sole instance of the document.
This is exactly what I am seeing. Pulling the document from the Trash and putting it back in the database’s Inbox, returns the replicant status for both instances.
A screencast of the behavior you’re describing could be helpful.