1. Make sure the repository folder which the database is linked to is solely used by SQL Source Control for that database (it's important to not manually add anything to the folder unless for troubleshooting purposes).
2. 'Partition Schemes' should not be filtered out from the repository. SQL Source Control > Set up > Edit filter rules:
3. Make sure "Ignore Filegroups, partition schemes and partition functions" is not checked. SQL Source Control > Set up > Comparison options:
4. Unlink the database from Source Control.
5. Delete the full contents of the SQL Source Control cache folder (%localappdata%\Red Gate\SQL Source Control 7\Caches).
6. Relink the database to Source Control and test.
7. If the problem persists, we recommend creating a new blank development database and using that instead; link it to the Database scripts folder in the repository and do a "Get Latest" to get the schema.
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