In case someone else runs into the same problem this is how I solved it.

In order for a fresh Guvnor installation to work against a pre-existing repository you need to add the following files to the appserver config directory (in the case of Glassfish /config/)

1. repository/repository/namespaces/ns_idx.properties
2. repository/repository/namespaces/ns_reg.properties
3. repository/repository/nodetypes/custom_nodetypes.xml

These files are generates the first time you deploy guvnor and let it create a new repository.

If someone knows why these files needs to be present for Guvnor to understand that it should use the existing repository instead of (trying to) create a new one I would be very interested to hear. Especially since the information in these files seem to be pretty static.

Best Regards

Mattias Avelin