Hi,
I'm not sure, but you may want to try with these other EJBQL queries:
SELECT OBJECT(cr) FROM CategoryRoot cr, Catalog ca
WHERE cr NOT MEMBER OF ca.categoryRoots
AND ca.catalogId = ?1
SELECT OBJECT(pg) FROM ProductGroup AS pg, IN(pg.catalogs) ca, CrossSellGroup cg
WHERE ca.catalogId = ?1
AND pg NOT MEMBER OF cg.productGroups
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