From bbeloff:

On the corrupted specifications:

After an archive is created, it may subsequently be corrupted such that it cannot be viewed in the Project archives window. At this point, it is still visible as deployed under the server, but it is absent.

The archive disappears from the list of archives in the Project archives view. The archive, if (automatically) updated at this point, appears to be empty. This is difficult to verify, because the problem can be transient.

I have made available the following:

http://www.classcalendar.biz/tech/packaging.zip

This contains two Eclipse projects with packaging specifications where this problem has happened several times. (Other projects in my workspace seem to be immune to the problem.) Note that I am not at liberty to include any sources or binaries for these projects.