Could you try rephrasing your question to be more illuminative about what it is you want to do? As written, I don't understand this question at all.
QuickTime will still let you listen to audio files at 2x speed if you want, and my exploration of iTunes 11 thus far does not show me any changes in the way app "documents" such as audio recordings are handled. I just transferred over a couple of interviews I did today, in fact, and last night I moved some converted video files from my Mac to the iPad in the same way as I've always done, so I'm not sure quite what you're saying.
Maybe if you described how the workflow used to work, that would be helpful. Also, as usual, it would be great to include relevant data such as:
1. What model of Mac do you have? What OS?
2. What version of audionote? Is it up to date?
3. What version of iOS are you running? On what device? Is it it up to date?