New adobe audition 2020 update not saving files in external folders

Thanks for the report. This will be fixed in the next release of Au. There should also be a public Beta of Au within the next few days that contains the fix as well. I’ll update this thread once that public Beta is available. 

Just to add a little more to this discussion thread...

Running AA 13.0.78, I've just completed the first "draft" of a podcast consisting of three spoken word clips and three music clips.  The spoken word clips were originally one file, "cut" into clips using highlight each clip and use f8 to mark it, then "Insert into multitrack".

The music tracks were similar clips, two taken from one file and the third from another, each of these files being a church service, so extracting specific music items, again created via the highlight...f8 method.

I inserted the speech clips to Track 1 of the multitrack, between the music clips (which were on Track 2) and almost instantly one of the speech clips went "offline".  (If I remember correctly, simply scrolling through the timeline provoked the "offline problem".)  It was quite easy to replace the offline clip with another copy of it (?apparently no method to "force" a relink to the original clip?) and then delete the "original" (offline) clip from the multitrack.

So far so good.  Except that the Files panel now shows two copies of the same speech file, not sure why?  I think the presence of these two in the list may be causing AA to throw the same error message as the OP gives, every time I need to save the project, even though ALL the media files ARE in the "Imported Files" folder already.  I tend to click "Yes", in an attempt to stop AA throwing the error message even though I know the specific file is in that folder (I did check!), but the "error message" keeps appearing.

Am I doing something obviously wrong, or is this an AA anomaly?

Shouldn't happen - but... even though you've stored a copy of the file in the session folder, that doesn't mean that it's the file that the session is using. If you keep the files you are actually using in the session folder and replace the external ones with those, it ought to work fine when you re-open it. Report back if it doesn't...