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Late last week I started noticing that I can't delete emails from either Junk or Trash folders in my Mail program. In addition the Mail program seems to run very slowly when sending emails and I cannot quit it and have to force quit.

When deleting emails, I highlight as many as I want, select delete and they disappear from sight. But when I return back to that folder they reappear.

In the console I am seeing messages like:

5/31/16 6:43:42.849 AM Mail[1305]: Skipping STATUS for INBOX.Deleted Messages because CHECK failed with error: (null)
5/31/16 6:43:42.851 AM Mail[1305]: Skipping STATUS for INBOX because CHECK failed with error: (null)
5/31/16 6:43:42.853 AM Mail[1305]: Skipping STATUS for INBOX.Deleted Messages because CHECK failed with error: (null)
5/31/16 6:43:42.854 AM Mail[1305]: Skipping STATUS for INBOX because CHECK failed with error: (null)
5/31/16 6:44:01.659 AM Mail[1305]: Skipping STATUS for INBOX because CHECK failed with error: (null)
5/31/16 6:44:01.840 AM Mail[1305]: Skipping STATUS for Trash because CHECK failed with error: (null)
5/31/16 7:04:53.590 AM Mail[1305]: Failed to open emlx and partial.emlx files (/Users/jdmobile/Library/Mail/V3/IMAP-[Redacted]/INBOX.mbox/Junk.mbox/CF2FBDC0-75B0-42CD-8443-70E3612FF687/Data/4/4/Messages/44436.partial.emlx)

In addition at times I have seen the Mail program using up to 10% of CPU and currently my Mail program racked up 46 minutes of CPU time and is consuming 26 threads.

Can anyone suggest what to start looking for?

Edit

Based on user6492's answer I really should add that:

  1. I can receive email perfectly fine on my problem El Capitan Mac.
  2. The email configuration for the IMAP account looks non-corrupted.
  3. Using another Mac that has Mail configured for the same IMAP account, I can send/receive/delete email without any issue. So the server side of the email equation has not changed.

Edit 2

Now it really gets weird for me. It appears that I can delete emails if I do it one at a time or even a few at a time - not sure at what point it starts to fail to delete

Edit 3 I managed to delete lots of emails from both the Junk and Trash folders, however I am stuck with 16 messages that I can't delete from my Trash folder and 1 that I can't delete from my Spam folder. All of the messages are marked as being Spam, and when I right click on any of them and say they are not junk mail, they remain tagged as junk mail.

I suspect that something down inside the Mail system is corrupt and not allowing these files to be deleted.

Edit 4

After a force quit I managed to manually delete all but one email. But this is a strange one and I think the source of all of my problems as it shows in both the Trash and Junk mail folders at the same time.

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You seems to have an IMAP account, so Mail order server to delete those emails, but something goes wrong and the task is not completed. When Mail sincronizes with server again, those emails will show up again because were never actually deleted from server. You have to review the configurations of this account with your mail provider - probably request for a support. I'm afraid this is the first step. Chances are your configurations changed somehow (even some corrupted file) or the server were updated and your configurations are outdated.

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    To improve your answer, please include the configuration file path. – Brick May 31 '16 at 13:28
  • I can receive email without a problem. And using another Mac the Mail program works correctly for all functions for the same account - so the server configuration has not changed. I'll add that to my question – Peter M May 31 '16 at 14:10
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After poking around and deleting various emails and force quitting Mail various times I finally figured out a fix to my problem, but I don't know the "Why" of it all and will never know.

I knew that there seemed to be one particular email that was causing trouble as it was the only one I could never deleted. I even tried delving into the elmx files in the Mail folder and deleting the file there - but that didn't work.

Eventually I realized that I had to delete the email at its source. So I logged into my IMAP account via its web portal, found the offending email and deleted it there.

From that point on the Mail app has been responsive and I haven't had any issues with deleting unwanted emails.

So somehow this one email was malformed to the point that the Mail app could not deal with it, but still managed to cause a lot of problems.

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