Emails disappear

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emails frequently disappear & i can't find them anywhere. I am running an iMac on ElCapitan.
 
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Need some more information:

1. Are you making backups to an external device?

2. Have you ever done any disk cleanup/maintenance/repairs, from a software perspective?

3. What eMail client are you using?

I wonder if part of the issue could be due to not permanently removing deleted EMails. I use Outlook 2016 as my EMail client, and I do just that everything I select an EMail to be deleted. There are 2 ways to do it in Outlook 2016, but I don't know how to do it with other EMail programs.
 
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I back=up to another drive.
Ihave recently run clean my mac 3. It had no affect on my email problem.
Client? I use the Mail 9.3 that came with elcapitan
 
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Clean My Mac can cause issues, from what I have read. It would be best if you got rid of it, and use another, more reliable product, like Onyx. It has been around for a number of years, has had numerous positive reviews, and is free! You can get it from here:

https://www.titanium-software.fr/en/onyx.html

Make sure you get the correct version.

Also, to remove Clean My Mac, here is another excellent product:

https://freemacsoft.net/appcleaner/

Again, works well, and is free.

Now, neither Clean my Mac nor Onyx will do any cleaning of EMails. I'll try and find out how to do that with Apple's Mail program.
 
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OK, it looks like the procedure to have deleted EMails permanently removed is:

"I had the same problem. Solved it by going to Mail, Preferences, Accounts, Mailbox Behaviors. Deselect 'Store junk messages on server' in Junk and Trash. Also select 'Delete junk messages' and 'Erase deleted messages' when quitting mail."

From what I understand, that first option, "Deselect 'Store junk messages on server' in Junk and Trash", only applies if you have an IMAP account with your ISP. I have a POP account, so that does not apply to my situation.

See if that helps.
 

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