I am only new at Kicad too.
It scares me when I change the schematic as I am afraid of losing work.
But I think you have to annotate the schematic as well, to get your netlist.
schematic, annotate, recreate the netlist, read it into pcbnew. Then just add the tracks.
There are annotate options here that can muck the netlist up, so be careful.
ps. Being a programmer I also use source control (subversion) on my Kicad files. .sch, .lib, .mod, .net , .pcb.
I find it is especially useful as most Kicad files are text files. So you can see more easily what the differences are.
I would recommend using source control with Kicad to everyone.
Does anyone else do this?