Audition is not finding all the session files.

No, it's not that. It has everything to do with the fact that, despite it being promised years ago, no direct linkage has ever been created between Premiere's Bin system and Audition. IOW give Audition Bins. My understanding is that actually, this is something that's quite complicated to achieve, but until something is done about rationalising a solution to this, there are going to be hiccups of the sort you're having.

Hi @SteveG_AudioMasters_,

Thank you for your reply, I think I almost understand what you’re saying, that maybe audition isn’t quite prepared to handle larger projects? 

If I've understood this correctly, you've run into the difference between Audition being linked to a Premiere session (and its resources) and an actual Audition session - they are definitely not the same thing! When you edit the Premiere session/project in Audition, it's a part of a (hidden) round trip process, and on that basis Audition doesn't need to know where all the resources are. To extract that as a separate Audition session, it would definitely help if all the associated files, or copies of them, were in the same folder. At that point you should be able to open the session in Audition with all the files in the correct place, and store that as a separate session - which you should be able to reference without anything missing.

At least that's what I think is happening - the round trip system appears to have its limits, and I think you may have run into one of them. In theory at least, it is still a work in progress. The way it was described to me (some time ago) by one of the developers was that the process could only really work the way it was intended to if Premiere and Audition were running at the same time and sharing resources - which is effectively what happens when you do the round trip thing.