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It has been observed that at sometimes Netbeans stops "recognizing" classes that are annotated as web services. It usually happens when re-opening the IDE but also randomly while editing the class. Although the web service icon appears next to the class name, the subfolder and the deployment information is missing.
In addition, the only way I found to fix this (until the next time it happens) is to copy the source, recreate the same class as a web service and paste the source back. The same source compiles without errors and the web service is deployed normally.
I'm not able to reproduce this.