I'm using mac mail v7.3 in mavericks on an iMac. I'm trying to trim the size of my inbox and SENT mailboxes using Message > Remove attachments. First I sort, say, the inbox by size to identify the largest messages. I select a message -- even a single message not in a larger thread -- and click Message > Remove attachments. Zing! The whole message disappears from the inbox. Then if I search for it, I find it in "All Messages", not th e inbox, and it still has the attachments! Same thing if the message started in SENT -- it gets moved to "All Messages". This is a pain because my goal was to strip the attachments, then save the message to a specific mailbox quickly and efficiently; I can't seem to do either!
You have a gmail account in your Apple mail.
Gmail has something called "All mail", where it automatically stores all mail.
When you enable that in the gmail Settings - Labels -
Show in IMAP, it will show in your Apple Mail as "Archive" folder aka All Mail.
If you disable it it will no longer show in Apple Mail, but it will remain in Google gmail.