euqaz, nice detective work!
I am not sure how much the locked JAR contributes to your earlier problem, but it definitely looks as if you have identified a bug in EclipseLink. This is not something that GlasFish can correct, so opening an EclipseLink issue (if there is not one already open for this) is probably best.
As you seem to understand, the warning message during deployment/undeployment says basically that the file used to be part of the app but is not a part of it in the later deployment. But because it still resides in the directory it might continue to be accessible to your application, which is typically not what people intend when they remove a JAR from an app!
- Tim
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