Ok, so I went back and dug up the conversations knowing I wasn't going insane.  Peter Hall said in one post that the Breakpoint information IS passed in the SWD:
The way the Debugger saves breakpoints into and XML or whatever is a Flash IDE Debugger specific feature. You could as well save them somewhere else. It's not part of the Protocol, it's just an implementation-specific way of storing a given configuration.
 
Nicolas
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