Reference is out of scope for generated nodes

I have a model which is generated dynamically. In the generated model there are references which are valid (I can click on them and they lead to valid targets) but are marked as out of scope.

If I press F5 the same references are not changed (they keep pointing to the same values as before) but they are not marked anymore as unresolved.

I am not sure why is happening and if there is a way to force recalculating the scope.

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