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Ryan,
It is curious to methe parts are "fine" as you describe if a parent has been deleted. I would bet at some point, during some redefinition of a feature that you will find the need to redo some references within features.
Regardless, try this simple old schoolPro/E slight of hand trick. Create a file(part or assembly)with the the original name of the parent model that was deleted. It does not need to have any geometry within the assembly. You may find that all the reference viewer is looking for is the name of the file. You can keep the new filetagged as contentand bring it into session when you load the files of importance.
It's worth a try.