Deleted files in the mail server will also be deleted in EM Client???

I deleted some emails in the server because it says that quota is reach. When I went back to EM client also my inbox has been deleted. Its not even i the trash folders in EM Client.huhuhu How will I be able to restore the files???

if you use IMAP mail system I am afraid it can be solved only on the side of server (some undelete there if possible, but probably not). If you use POP system, mails are always downloaded and stored locally at your computer (em Client).

Its actually using IMAP as EM Client configured it automatically when we set up the account. Unfortunately, I looked at the server and no traces of the deleted files ((trash,etc). Is there other way to retrieve it?

No, it is not possible and eM Client only displays what is on the server.

(You can contact an administrator of your server, there is small chance he/she will have some backup.)