We had a support case where a user running JIRA EAR/WAR was finding that everytime they deployed the WAR their logo would disappear. This was because they were making changes directly into the directory where the application server (Tomcat in this case) expanded the WAR.

http://www.atlassian.com/software/jira/docs/latest/config_overview.html reads

The build.xml file is an Ant file, which when invoked with the build.(sh|bat) script, will construct a deployable webapp. build.xml does this by copying the contents of the webapp/ directory, and overwriting it with the contents of edit-webapp/. Thus, never edit files in the webapp/ directory!. If a file needs editing, first copy it from webapp/path/to/file to edit-webapp/path/to/file, and edit it there.

I think this should be updated to include an additional note that any plugins / images etc must be built directly into the WAR in the same manner, and a warning to never edit anything directly on the server.