... but starts to break down once you get into the acceptance testing phase--it's hard to write stories for invidivual bugs until you know they exist (which means that the amount of stories in the phase can keep growing) and it's very hard to estimate how long it will take to fix a particular bug.

If you're finding a lot of problems during acceptance testing, you've got bigger problems than velocity.

What kind of problems are you seeing?

• "That isn't what I wanted!" problems mean that you aren't communicating with your customer early and often enough.
  
  
• "It doesn't work!" problems mean that you're either slipping on Test-Driven Development, and aren't getting adequate test coverage, or you're giving in to time pressure and letting quality slip rather than deferring stories into later iterations.
  
  
• If you're finding it "very" hard to estimate how long it'll take to fix a bug that's slipped through into acceptance testing, then you probably have a large design or refactoring debt that's cluttering up your system. Are you taking the time to refactor?

Problems with velocity during testing are symptoms of upstream problems. Identify and fix the upstream problems, and your downstream velocity problems will take care of themselves.

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