Mac Mail removed content from folders, brought back Archive folder

For the last two weeks, I've had no issues with Mac Mail on my new Macbook Pro running Mavericks.
My Mac Mail folders (not folders on the gmail side) were using my rules and filters accordingly. All of a sudden, without warning, my folders went completely blank.
I was using Mail's rules to send messages from Google Alerts to a folder, then things from Twitter and Facebook to another folder and I moved some messages into a third folder for future work.
The "Archive" box was not visible ... now, the Archive box has returned and there are no messages in my folders. I had about 45 unread google alert emails that are no longer showing.
I thought this was fixed because I went back to Mac Mail from Thunderbird to give it a shot. Worked fine with my gmail account. Now, it's back to being buggy again.
I've tried many other mail programs, but Mac Mail was by far the most productive for me. I've shut down and restarted and had the same thing.
The ONLY thing I've done to Mac Mail in the last 2 hours before it started was change a link in my signature and saved it. That was it. Unless that's the bug, I am pulling the rest of my hair out having these issues with Mac Mail. I do not use the web version of gmail very much because it just doesn't suit my workflow. Mac Mail was working great until Mavericks, then I got a new machine and after about two weeks, I tried it and it worked exactly like pre-Mavericks releases.
Now I've lost a bunch of folders and have no idea where those messages are. They were moved and are gone. Whiskey Tango Foxtrot is going on here.

Seems like it storing the same emails in different folders . As i see now :
All Mail 5.11 GB
Inbox     2.82 GB
Important 2.56 GB
Sent Mail 1.8 GB
Sent          767.4 MB
Starred     482.4 MB
Drafts      57.4 MB
Trash       9.7 MB
Junk e-mail 671 kb
Bin              414 kb
Spam      0
Deleted Items   0
Apple Mail To Do 0
Priority 0
Follow up 0
Misc 0
from this above , i can understand that Inbox ( 2.82 Gb ) and Sent ( 767.4 Mb ) and Drafts are real folders that contains actual files according to the current status on server .
what the **** the other folders contains , i can not get. I though those folders should have just show the same files available in the main folders , in different way, according to Folder focus. Am i right ??
apparently i suspect they just copied original files for some purpuses, insead of working as simple filter folders.
can anybody explain me , how to work this out and make my Mail app do not dublicate emails , but store them in appropriate way and show it to me .

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