As an RX3 user myself, I can feel some of the pain in this. It's the same with any externally processed file, and yes, a simple (but inherently dangerous) 'replace' command would go a long way.
My approach to this though is different. I do all of the processing necessary first, before anything gets anywhere near multitrack view, and sidestep the problem completely. With RX3, the processing time has speeded immensely, so even attacking large unedited chunks isn't such a pain now. Indeed sometimes it's an advantage to have the whole file available - you invariably get more choice in what you can select as a background reference, and if you have that choice, it's the way that the RX NR works best.
Had I known Audition didn't support such a feature, I too would've done the offline editing first. I'm also a Sony Vegas user, and it has such a wonderfully intuitive interface. I can select a clip in the Vegas timeline, send it to any application I designate in the options, save it in the offline app after making changes, and bam. Vegas automatically creates a new take of the processed clip. I had just assumed that Audition would have a similar feature.
The only problem is that, for whatever reason, Vegas shows clipped waveforms (and the tracks also clip on the meter), even though the source audio is NOT clipped. (Pulling the same tracks into Premiere Pro, Audition, Sonar X2 results in normal, unclipped waveforms, no meter clipping.) It is truly puzzling and frustrating, because although I spent several hours chopping the source audio tracks into clips within Audition, I'm thinking the best route is to do what you suggested and process the clips first, then bring them back into Audition for the rest of the mixing process. But since I don't want to bring a 90-minute track into RX3, using the nice Vegas interface to process individual clips would be the best route, but then I'm dealing with clipped audio that isn't really clipped.
Once you've converted the clips to a unique copy and saved them to disk, you could open those new files in RX3, perform your changes, and save, overwriting the file on disk. This will change the raw assets on disk and should update the clip contents in Audition without requiring relinking, though you might want to back them up prior to modification in RX3 in case you wish to revert back.
Which version of Vegas are you using? All my audio clips from Audition appear at the correct level when imported into Vegas, no clipping either on the track or on the meters. Your Vegas Master channel fader is set to '0dB' not at the top. There is 12dB extra gain available with the fader right at the top.
Just as an FYI, I've done the procedure Durin mentions (though not for RX3--you guys have more money than me!) and it works well. I'm paranoid enough that I do a "Save As" on the clip I'm copying to new just to make sure I still have the original but I don't think I've ever had to resort to using it.
It's a bit of effort but it works.
Yep, thanks for the feedback. Turns out I was making more work for myself by opening the unique copy in the waveform, selecting all, then saving as another file to manipulate in RX3. I just tracked down the default location where Audition stores the bounced clips, and lo and behold, there were all of the unique copies I created. Shut down Audition, opened the files in RX3, fixed them, and saved them. When I opened the project again in Audition, it pulled the new versions of the unique copies, and there you have it. Denoised clips perfectly in sync.
While I'd much prefer to have an easy, streamlined (and non-destructive without manually making backups) process like what's available in Vegas, I'll take what I can get.
(And to address the Vegas question, I'm using Vegas Pro 10. But since this is the only time I've noticed that in Vegas and I'm able to manage the workflow between Audition/RX3, I won't concern myself with it for the time being!)
Thanks for the help.