Saving reference edits is distinct part of a referencing workflow that you can use to 'bake' the reference edits you made to a referenced file back into the original referenced file. After you save the reference edits back into the reference file, they are permanently part of that referenced file. At this point, the concept of them being reference edits no longer applies since the original file has been permanently changed.
When saving reference edits, consider the following:
What gets saved to the reference file
Edits that are applied in the parent scene, specifically setAttr, deleteAttr, and addAttr, as well as commands that create and remove connections within the same referenced file, specifically connectAttr and disconnectAttr, are saved as part of the Save Reference Edits operation. Nodes and connections from the parent scene that affect only nodes from the referenced file will be saved to the reference file. For example, construction history and textures that affect only the reference file will be saved into the reference file. DAG nodes such as shapes from the main scene will never be saved to the reference file, with the exception of new construction history shapes that are parented beneath transforms from the reference file.
If you require new DAG nodes to be written out as part of the save reference edits operation, you can import the referenced file so all of the items reside in the scene, and then select only those imported items as well as any new nodes, and export the selection as a reference again. In this way, all of the edits to the nodes and attributes will get written to the exported file reference. See Export file references
Importing and then exporting a reference has the potential to introduce namespace conflicts for other scenes that subsequently reference the exported reference. It is recommended that you remove any recently imported nodes from their old namespace prior to exporting a reference. For more information, see Remove namespaces.