I have a project where some of the audio clip or clips became corrupt. The audio engine would stop at that point. I was unable to bounce it, and couldn't finish the project as is. Tried everything.
 
Then I exported it as a bun file under a new name (retaining the old file as a backup), and then opened the bun file. When I played it there were odd sounds at some points.  I pinpointed this to about 6 short clips which I had tuned with Melodyne, and had bounced these to clips so they were no longer Melodyne clips (I thought).  All 6 of these clips were bad in the new project ... some had 'become' other audio clips from the project, and some were just flat-line silent.
 
Outside of Melodyne, I also had similar problems with a few loops I had imported into the project (these are percussion loops I made over the years and have used many times in other projects)
 
Luckily I had kept the corrupt project (where most of the audio was still good). I was able to replace the bad clips by copying from the old project.  So I'm back in business again.
 
My question is - can Melodyne'd clips be exported to bun and back again?  I'm a bit concerned about using Melodyne in the future.

I'm pretty sure this has come up before, and that you need to bounce Melodyne files before saving as a bun. I don't think you can save bun files with the Melodyne Editor active on tracks. I'm sure others will correct me if I got that wrong. [It was wrong, see below]
 
I recommend saving using per-project folders, and using bun as a secondary backup or for file transfers with others. There is nothing inherently wrong with the bun format, but they're like zip files - if one bit gets dropped due to file transfer problems or storage media issues (e.g., a cell failing in a flash drive), you will likely not be able to recover the file. With per-project, you'll be able to recover everything except for the specific file that was corrupted.

Thank you Craig!  
 
I did bounce the Melodyne clips before saving to the bun. 
 
I do use per-project audio files.  I rarely use bun files. Just did this time as a last-ditch effort to repair a project with some corrupted audio that wouldn't bounce down ... and thankfully the bun maneuver did save the project.

There is no need to bounce ARA clips before saving bundes. All the Melodyne state is stored inside an ARA archive that is written as part of the CWP file. When you save a bundle it is exactly the same as saving a project in this regard. 
Bundle files don't do anything special to ARA regions since they are treated just like other audio clips.

Sorry about that, thanks Noel. I tried to find the reference about some kind of restriction with BUN files, but couldn't.

Thanks Noel, that's good to know.
 
Perhaps it was just an oddity with this one project if you've not seen this happen with other users.  The only clips that were 'corrupt' after opening the bun were clips that had been processed by Melodyne (although they had been bounced [rendered?] "pre-bun"), and a few of my self-created loops (like a couple measures of eggz shaker ... which have been reliable in the past).