Re-annotation from pcb now means my components are linked with different designators
You now need to back-annotate the schematic. When you re-annotated the board, it should have generated a &quot;.was&quot; file (most likely in your project directory). Within the schematic, you now need to go to Tools --&gt; Annotate --&gt; 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.