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Accidental annotation of schematic, update net in PCB editor?

Ruddwijk

So i've run into a bit of a rut. I renamed some connections in Capture, the hierarchical block had to be replaced, whereas netlist generation was impossible because of duplicate refdes for all parts in the block (although there was only one in the design and no actual duplicate parts?). As i saved a copy to edit, i had the wrong project file selected as i did an annotation and now i have a hard time back annotating or redoing the list without placing all the components over. 

Is there any way to clean up this mess in an orderly way? Or manually edit the small details needed in the netlist? PCB editor 17.2

Thanks

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