recreating:
1. You have scene *B* with referenced object *pCubeRef* that has no namespace (merge option).
2. You have main scene *A* with let say *locator1*.
3. You referencing *B* into *A* without namespace (merge option). And doing some edits (eg. binding, constraining and connecting), let's make parentConstraint from *locator1* to *pCubeRef*.
4. Make copy of *B* > *B1* and import reference of *pCubeRef*.
5. Switch to *B1* in *A* scene.
After you merge reference inside scene B, and updating it in scene A, some edits on that merged reference became lost, however the reference editor shows them as successful.
Thus applying failed edits nor changing edit targets not helping at all.
Any thoughts how to revive those edits?