The refresh call is the same, i.e.: it uses the same logic to refresh the catalog. Do you have multiple catalogs in your project and you refresh just 1 unattended? Do you by any chance login differently when you refresh manually?
What does 'most' mean, you only keep the custom relations? Could you enlist the preferences settings you've defined under 'Catalog Refresher' ?
When I refresh northwind unattended, it keeps all its relations...
My settings:
- AddNewElementsAfterRefresh: false
- AddNewViewsAsEntitiesAfterRefresh: false
- CreateBackupBeforeRefresh: true
- ShowReportAfterRefresh: true
- SyncMappedElementNamesAfterRefresh: false
- UpdateCustomPropertiesAfterRefresh: true
- VerboseRefresh: false