I have a project and war archive.
The destination of this archive is our production server.
Once a week i do manual build and war is deployed on server.
( option "Enable incremental builder" is OFF )
But sometimes i do "clear" project ( Project-> Clean)
, and then my war is cleared from server (application is undeployed)

Maybe this is not bug. But this means that I can't have project arhive in my project and every time I must create a new one.