The relationship in the DB is not a requirement. It is used by the designer to infer the relationship "properties" you get automatically, but you can add your own and indicate which scalar properties identify the relationship in both tables. (Right click on the designer, choose "Add Relationship" and identify both tables and columns, or drag/drop with the "relationship" tool)
Be careful though. If your problem is that the application stores "placeholder values" to identify "no relationship" (like a zero value that has no counterpart in the primary key table), you might end up with exceptions being raised if you try accessing the corresponding member in the code.
If the problem is that the original application stores stuff in the wrong order (therefore preventing you from enforcing an FK constraint), but when all is said and done you have consistent data, then you should have no problem.