Audition CS6 - Replacing Clips

Question

Hello all.  I'm using Audition CS6 to create a stereo mix for a feature film.  I inserted the picture-locked video for sync/reference, then added all of the dialogue, SFX and score tracks.  I went through and chopped up each track into clips, ready to rock. 
I'm using a third-party application (RX3) for noise reduction, and I'm trying to edit individual clips offline so I can apply the noise reduction/spectral repair/etc then bring the fixed clip back into Audition.  Unfortunately, the plug-in version doesn't work very well so editing the audio in the standalone version is what yields the best results.  The problem I'm running into is that when I bring the clips back into Audition, there doesn't seem to be a way to line up the new clip with the original.  If snapping is enabled, it rarely lines up exactly, which means my dialogue will be out of sync.  If I turn off snapping and try to do it manually, Audition automatically inserts crossfades between the two clips.  Here's my workflow:
Select clip within Audition
Right-click>Convert to Unique Copy
Double-click the clip to open in Waveform Editor
Double-click to Select All
Right-click>Save Selection As
Open the newly saved file in RX3, apply fixes, then save.
Drag new version of file into Audition, on top of original clip.
Sometimes it lines up perfectly without crossfades; usually it doesn't.
It's a ridiculously tedious process, but I can't for the life of me find a "Replace Clip" option, whereas I could simply select the original clip in the Audition multitrack timeline, use a replace function, point to the fixed audio file, and done.  That feature would eliminate all of the sync/crossfade problems I'm having, but I haven't figured out how to do it.
(Yes, I'm aware that Audition comes with its own noise reduction tools, but truth be told, I've found RX3 to be easier and more effective.)
Any tips on how I can export a single clip out of Audition, fix it offline, then bring the fixed version back into Audition to replace the original clip while keeping everything in sync??

Answer 1

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.
Ugh!