You could set the Auto Rename flag in the PCB Editor Configuration Manage to allow changes to only those parts you want to update. Then you can specify how you want the parts renamed before you run the auto rename function. After running that then back annotate those changes into Capture. You may have to do this several times if you schematic is several pages........ Save your board and schematic to new files (or backup your existing files first......) Then generate a new netlist and load it into the board before trying the renaming. Doing this will link the two files together and will allow the back annotate to function properly. Have Fun!
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