gmail's understanding of IMAP and Apple Mail's understanding of IMAP are not 
the same, and if you're not careful this can produce funny results. The way 
they both work is rather complicated. Thankfully, Joe Kissell has written a 
number of great MacWorld and TidBits articles which are free on the web, as 
well as two fantastic books called Take Control of Apple Mail, one for Mountain 
Lion and one for iOS devices. I highly recommend both books. I thought Mail was 
a pretty simple thing and I knew all there was to know about it. How wrong I 
was. The books are brilliant and really help you to avoid problems like the one 
you're having.

There are many possibilities of what's going on at your end but it's probably 
got something to do with your settings on both Mail and gmail for how to treat 
deleted messages. Archive them? move them to the trash folder? Keep them on the 
server or store them locally? Expunge them immediately or later? Etcetera. 
Again, I really recommend Take Control of Apple Mail or that you at least 
google Joe Kissell Apple Mail and gmail.

Best,
Nic

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