FInstancedStructs, or its TInstancedStruct sibling, can be included in a class that inherits from UDeveloperSettings. UDeveloperSettings will persist data in a configuration file.
In the case of FInstancedStructs properties, only the default values will be persisted on disk. Modifications to those values in the editor will not persist. Modifications of the ini will be correctly read.
Create a UDeveloperSettings class with a FInstancedStruct or a TInstancedStruct and one base struct.
In the UnrealEditor, set the struct instance to the base struct and modify the values. Repeat on the base struct in the developer settings.
Upon closing the editor, the ini file will contain the default values of the struct for the instanced version, but the expected modified values for the base struct.
Furthermore, updating either set of values in the ini file will be correctly reflected in the editor.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-277466 in the post.