Six tennis balls with Vans shoes in the dryer worked well.
Oopps - my bad!
It actually worked pretty well. The flap is still a bit stiffer than I would like, but the tennis ball/Vans shoe beating -- after a fabric softener soaking -- definitely softened everything up nicely. Regular use will take care of the rest.
The best thing is that, the bag now looks like nothing anyone would want to try to steal (logos cut-off, canvas looking worn). It's important that my camera bags are both functional, and don't look like they are holding $20,000 worth of gear (a pair of M9's, lenses, etc).