Update 1
If you are familiar with Unreal Engine 4 or Unity you probably know bother use a prefab system and changing one object will change all of them. That’s obviously a time saver for scripters and modelers, especially when you may have 25 to 100+ of the same thing you want to change.
I’m not sure how much this will help you but I’m trying to get close to that prefab system as possible. You may not like how it is working currently though.
Currently it just relies on the Source copy to have a PrimaryPart, it doesn’t have to be at the bottom of the model I just chose to do that. All the copies must also have a primary part, or at least a “base” part so the script knows how to orientate the updated copy of the model.
The models being updated have the name of the Source model.
If you would use this let me know and what you would like it to do/be flexible with so it suits your workflow. All models be updated have to be in “Reference” and all source models have to be in “Source” currently. This will change once later to only rely on updated References through the new Tag system.
Update 2
Now a Tag based system so you no longer have to worry about grouped models or individual duplicates.
Summary

Moved to ReplicatedStorage.
Now a button for Refresh instead of a UI.
Still going to work on hotkeys such as maybe Ctrl + R for refresh, requiring you to select what prefabs you want to refresh or else it will attempt to refresh all prefabs at once.
The great thing now is you no longer need to have a name based system, it will update all tagged objects with the source prefabs tags.
Ex: WoodenBox can contain tags: “Shore Box, Facility Box” and all objects containing those tags will get refreshed.
Still working on make it not delete the original object and instead just replace it’s children.
Update 3
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Supports multiple copies through a folder.
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Moving or deleting a prefab will prompt a message if you want to delete all references.
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Renaming the prefab will update all prefab tags of all instances related to it to match the new name.