Stuck in Alert State

The "Error with file" did go away with the update, but that doesn't answer Ken's question.

I am getting the same message.  When I quit Protools it saves all the assetts in the appropriate folders (audio, fades, session) and CLOSES.  Closing Audition always seems like an ordeal.  Between all these dialog boxes, "Audition is getting ready to quit,"  and pop-ups including these strange error messages.  I really like this software but all this does not instill confidence. By asking if I want to replace every source file (one at a time) with the edited version in my session there is a high risk of erasing or replacing something that should not be changed.  So 2 questions:

1) What does this warning mean and where can I find the alert state it's referring to?

2) Other than while exporting, is there a preference for always saving every associated file WITH the session while leaving the source files safely alone?