The PercentDone component is very simple and doesn't officially support changing the percentage displayed. There are two work arounds:
Create a new PercentDone component
You can destroy the existing one and recreate it:
this.down('rallypercentdone').destroy();
this.add({
xtype: 'rallypercentdone',
percentDone: 0.5
});
Update PercentDone by touching its internals
This is technically bad as you are diving into the component's implementation, and we may change this in a future release of the SDK, but it's also better than a full destroy in my opinion:
cmp.update(cmp.renderTpl.apply({ percentDone: 0.5 }));
I'll make a note that we should flesh this component out some more for a future release.