Hello,
Just to clarify, VCS agent will surely take all the actions before declaring it faulted....
So if file is deleted.... Agent will detect that something happened outside to VCS (here you should see message in Log like, "resource become offline unexpectedly on its own, followed by resource is offline (not initiated by VCS) ), I wouldn't expect VCS to declare the fault until next step mentioned below is completed...
As soon VCS detects it, it should first complete 4 monitor cycles (by default) & then call for a clean action... If 2 attempts of clean also fails, resource should be declared faulted...
Do you say that even after clean is called, agent is not faulting the resource ?
Gaurav