When linking a database to a SQL Source Control project folder to an existing database you should try to ensure your project folder is synchronized so that it doesn't have any conflicting objects with your database, if not you'll hit current limitations. 

If a conflict is present when linking:

• For most cases, you'll be able to resolve the conflict after linking completes
• If there is a conflict on an object that is depended on by another non-conflicted object then you'll need to resolve this first outside of SQL Source Control before linking. For example: a conflict on a partition function that is used by a partition scheme.