Is the subdir a subirectory of inbox or a different subdirectory? Just to 
double check, is it maildir or mixedmaildir account?
Can you check that after the move (but before refresh), is the mail still 
physically on the disk in the inbox folder? You can check the location in the 
account settings, and locate the mail file e.g with a search in content on the 
file system.

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https://bugs.launchpad.net/bugs/883459

Title:
  KMail duplicates emails

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