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I'm afraid there isn't. Not without unlinking and relinking anyway.
Can you tell me a little bit more about your custom objects? Are these for different versions of production (e.g. for different customers) or for dev/test databases? Are we talking about schema or static data differences? What sorts of objects? Tables, sprocs etc? Do you have handy naming conventions?
There are clever things you can do with filters and post deploy scripts etc. For example:
https://www.red-gate.com/hub/product-learning/sql-compare/how-to-build-multiple-database-versions-from-the-same-source-using-sql-compare-filters
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We would like to attach Source Control to a single database that contains standard objects from one repository and database-specific custom objects from another.
Is there any way to Source Control our standard objects with the framework repository and associate the database-specific objects with another repository?
Thanks!