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After placing my components I re-annotated from the PCB to get positional annotation. This worked fine. But I've just noticed that components on my PCB and schematic (whilst linked, i.e I can click on the component on PCB and it will highlight it on schematic) do not have the same designators! R39 on schematic is linked to R40 on the pcb!

I tried doing an update schematic from PCB but it isn't picking up any changes?

How do i fix this??

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You now need to back-annotate the schematic. When you re-annotated the board, it should have generated a ".was" file (most likely in your project directory). Within the schematic, you now need to go to Tools --> Annotate --> Back Annotate Schematics and browse for the .was file.

This is from memory, so some of the paths may not be exact, but should be enough to get you what you need.

Following the back-annotation of the schematic, make sure to push your changes back to the PCB to ensure all nets are properly annotated and synced as well.

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