No it didn't. Compact will have created a new index and demonstrated to you that what you thought you had really no longer existed. But it did not delete or loose anything.

Look in your anti virus programs logs for quarantine and deletion of a file called inbox. It will have occurred about the time your mail cuts off. sso if you have say the last months mail the scan that removed your mail will have occurred about a month ago. For some reason users of Norton products appear to be particularly affected.