Deployed EAR project looses META-INF/application.xml

After working a couple of days with JBoss Tools and doing hot deployment of the EAR project the deployment doesn't work any more. Both META-INF/application.xml and META-INF/jboss-app.xml aren't copied to the exploded ear directory any more.

I tried
a) eclipse -clean
b) Disabling the JBoss Tools, restart Eclipse, (re-) enable JBoss Tools
There is no success.

The only solution was
1) Delete <workspace>/.metadata
2) Delete all subdirectories in eclipse/configuration so that only config.ini is there (as it was after unzipping eclipse)

Hmm, same procedure in 3 days? Probabely yes, according to the same observation by my project collegues.
I know about the vague description. However, I've no idea how to provide more information.