Automatically numbering elements in Kicad
I am using KiCAD 5.0.0 and as I refine my board design I often open Eeschema's Tools -&gt; Annotate Schematic dialog and select the Reset existing annotations option.  After doing this I load the newly generated netlist into PCBNew, making sure to select the Timestamp radio button in the PCBNew Netlist dialog. The Timestamp option tells PCBNew to select footprints based on their timestamp opposed to using the reference number which is the "normal way".  This allows PCBNew to know that what was R17 is now R12, what was C4 is now C2, etc.