The Remove Duplicate Particles tool is used for removing particle picks based on the input micrographs (e.g. for when you use two different particle pickers on the same micrograph, and want to combine the picks without any duplication via eliminating pick locations are close together).
If you’ve done multiple heterogeneous refinements, you should be able to take the output particles from all heterogeneous refinements (even if there are overlapping particles) and connect these to any downstream job without worrying about whether there are duplicates across the inputs. All jobs that take particles as inputs will also take the union across the inputs, while ensuring that particles with the same UIDs are not duplicated. Let me know if that makes sense