I am very experienced with Protel SE99 and excel spreadsheet BOM's.
My proposal would be to allocate a block of numbers for each board, e.g 0-100, 200-300 etc. and add this to the existing component references.
The board with the most components (AutoRPM) can be 0-100, then say 4046VCO was next R1 would become R101 etc. This way you can still relate it to the other board. Or adding an A, B, C etc. suffix is another way.
Modifying the gerbers is a non-starter as gerbers are just text files with primitives ( lines and arcs) so there is no text as such.
Access to the schematic files would be best but if not available then can just change on the PCB and regenerate gerbers.
Can start immediately as I have another design (4 layer using PFW 99SE) that is at pre-pod stage and I have a gap as I am waiting for some components and firmware to carry on testing.
I am also familiar with the components on your panel which helps when generating BOM's.
Happy to discuss and show some of my previous work.
Just had a play with PFW SE99 and it looks like all the designators have to be changed manually, I have some example files for the 4046VCO board but doesn't appear I can attach them to this message.