It is very difficult to answer your "has the Government ever" type question because that type of action wouldn't be captured in any centralized database.  I can confidently say that regulatory procedures are generally written to protect the Government and waiving audit rights and record retention requirements would rarely be in the Government's best interest.  Paragraph (f) of the clause at FAR 52.215-2 (f) has a "shall" statement that pertains to a contractor maintaining records for a 3-year time period in termination actions.  "Shall" statements are imperatives that can't be disregarded without regulatory exceptions to those mandates.  FAR 49.107 also uses a shall statement to have the Contracting Officer refer a contractor's termination settlement proposal to the appropriate audit agency.  DFARS PGI 249.105 then prescribes that a Settlement Memorandum should address why, if applicable, an auditors final report wasn't available for the settlement agreement.  And finally, FAR 49.105(c)(15) reminds the Contracting Officer that current, accurate, and complete data in the settlement proposal were essential for the Government to reach their fair and reasonable determination.  This certification gives the Government recourse if defective pricing was submitted and impacted the settlement amount.  So while a final audit, even after the settlement, seems excessive, it's just one more part of procedures that are designed to protect the Government.