Replication fails because of a non-existent foreign key
Sorry for waking up this dead thread, but I hate it when questions remains inconclusive. 
Anyway, I had the same problem. Apparently SQL server replication saves foreign keys in "dbo.MSsavedforeignkeys", which is where I found my blocker FK. A quick delete dbo.MSsavedforeignkeys where constraint_name = N'FK_TableOnlyInDestDB_MyReplicatedTable' solved my problem. Of course, there may be more "best practice" ways of cleaning up after failed replications.