Or does PCB have a method to reload all footprints?
Having had to do this myself once, I can easily say that you're
screwed. Here's the best you can do:
* Manually redo the traces near the footprint in question such that
replacing the footprint results in the same connectivity. In my
case, I was widening a SOT-20 so I had to pull the traces away and
straighten them, such that they passed through both where the old
pads are and where the new pads would be.
* Cut the old footprint out.
* Paste in the new footprint.
* Edit the traces to remove the bits that are no longer needed.
Option 2 would be to cut out the footprints and delete the traces that
led only to them (although pcb has no option to automate this), and
rerun the autorouter.