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I have two accounts set up in Mail 6.2. Most of the time I disable one of them (my personal account) to avoid being distracted at work.

Strangely, the number of "Flagged" messages includes messages from disabled accounts.

One flagged message? No, none actually.

Perhaps this is useful for someone, but it's unwanted behaviour for me. Anyone know how/if I can stop this happening?

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You've found a bug with Mail. I've just confirmed it fails for me as well. The count reflects the sum total of flags - and doesn't get filtered down when you disable an account that contributes to the total flag count.

I'll send a bug report to Apple and anyone else that cares can as well:

http://bugreporter.apple.com

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... and should I find a workaround, I'll post it, but this might be something we need a code fix for unless it's decided that somehow that is the correct behavior despite the badge not matching the filter of visible messages when this happens. –  bmike Jan 30 '13 at 23:08
    
Ah, great! So I'm not completely insane. I worry though, that perhaps this by design. I can't make a clear case for it, but perhaps some people think that flagged messages are so important that they should be always reminded that they exist, even in accounts that have been disabled... –  aaaidan Feb 1 '13 at 0:24
    
No - if Apple felt you shouldn't hide a flagged message, they would expose it so you could see it or pop a warning when you disable an account with a message flagged. Not mess with this number doesn't match the count business. This is a bug and not a feature. –  bmike Feb 1 '13 at 1:32
    
Can confirm it's a bug: when I restart Mail, it goes away. –  aaaidan Feb 6 '13 at 21:53
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