Archived mail keeps reappearing in Inbox on OS X
Archived mail keeps reappearing in Inbox …


Smells of a database inconsistency. 


  I rebuilt the mail database by deleting the Envelope Index files from /Users//Library/Mail/V3/MailData/


Critically: 


did you quit Mail – and allow time for completion of that quit – before those deletions? 


Some of the many articles about Envelope Index lack that recommendation. Here's one of the better articles: SpamSieve Manual: How can I rebuild Apple Mail’s database?

Cross reference

My reply to a MacRumors Forums topic that appears to involve a database inconsistency.