Did you create the schematic in Eeschema? There you can automagically change the name of the instances and that will translate to Pcbnew in the net list.
Yes, they are all in eeschema, and imported through the netlist.
They all appear in PCBnew, of course.
What I'm trying to do: have them neatly arranged in an array.
So I tried the "Create Footprint Array" feature.
"BUT," you might say, "if there are LED footprints D1 to 64, you will make duplicates!" To this I'd answer that I tried doing so, having beforehand deleted D2 to D64 beforehand. (And I also tried without removing them).
My problem is that the footprints generated by the "Create Footprint Array" tool all have the same reference.