Okay, I have found the problem.
I have moved the xref-plugin configuration (including the dependency that contains the stylesheet) to the pluginManagement section.
While this works for the javadoc plugin (also has an additional dependency declared and references the resource) it does not for xref.
So I had to move the dependency back to build.plugins.
Now it works as expected again.
I don't know enough about maven and plugin configuration to find out whether this is a bug or my fault... I assume the second.
At least a better error message will be very helpful...