You can use the “top ###” qualifier in the QueryBuilder query to force it to return any number of records, it just defaults to 1000. I used the following query to get a list of all repository objects that had files associated with them. The actual file repository location(s) are shown in the “si_files” result set.
SELECT top 64000 si_name, si_kind, si_size, si_files, si_id, si_instance, si_owner, si_creation_time FROM CI_INFOOBJECTS WHERE SI_FILES > 0 order by si_creation_time