auto archiving, messages lost

I enabled auto-archiving on my gmail account.

Messages are gone from my server but I see empty folder on the local. 

Kanwaljit, I was hoping a GMail user might have replied to your question, as I am not regularly using that provider with IMAP, and my experience is limited.

Did you try and search for one of the archived emails in eM Client. That might indicate where it is.