Well, LLBLGen Pro only READs metadata it never creates / writes meta-data.
How do you manage your databases? In a 3rd party E/R model tool or something? It might be you make a change there and forget to update relations or something or create a create script which drops everything but doesn't re-create the constraints. For example in sqlserver when you create a create script, you have to explicitly enable FK/PK constraints generation into the script.