There are three ways your message rules can be deleted or hidden.

• If you linked your listings, Host Tools will hide all the "child" listing's message rules and use the "parent" listing's message rules.  Typically this is very easy to fix, just unlink the listings and re-link them but make the "child" listing the "parent" listing.
• If you deleted your message rule
• If you deleted your account, Host Tools will also delete all your listings and message rules that are linked to that account.