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Note: The Joiner table has 2 FKs, one FK for Sample and the other FK for Method.
If sample method is your join table, then your data model is wrong; the JT needs to be directly related to both parents via FK = PK, so
Sample --< JT >-- Method
You need that Method table occurrence in addition to the Cartesian one you use as selector; that latter is for your user interface (show all methods), but the first one is a structural component (tie a reference FK to its source PK and give direct access to that entity).
Another quick question, why is there a need to duplicate the Joiner table and save to that?
Only if you want to a) create related records via a portal, AND b) have a portal for display where the user should be able to edit, but not add records. Since the ability to add records in a portal is a relationship setting, you would have two relationships (and need two TOs of the target table) that are identical except for that setting.
There are other methods to create related records, so this isn't a necessity.
Thanks, updating my JT to add another reference to the Method table's PK worked.