I had the same problem.

In my case I wasn't using the default data dir, and what happened was that
the data directory was updated with incomplete data staying in an
inconsistent state.

When tomcat starts, and geoserver starts, it (geoserver) looks at the
gwc-layers directory and if it finds any layer file (xml) that is not
mentioned elsewhere on other files, it removes it.

This behavior can be seen in geoserver.log if you pay attention to it when
tomcat restarts.

I know this thread is kind of old, but hope this can help anyone in the
future.



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