Found the problem, so to answer my own question:
If you want to use existing wsdl in your webservice and not the ones glassfish is producing make sure you ejbmodule inside an ear (didn't test outside) contains only one period. Upon deploying the last period is replaced by an underscore, but on wsdl creation all periods are replaced by an underscore leading to two separate directories.
Now it works like a charm when placing the wsdl and xsd files into META-INF/wsdl.
Johan
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