Does an ACO now have the authority to modify a contract if the total amount of the mod lies within his warrant threshold without regard to absolute value of the additions and deletions?
The USACE Acquisition Instruction (UAI) uses terms like "obligate" and "individual contract modification" to outline the limitations of an ACO's warrant. FAR 1.602-1 and FAR 43.102 reveal that the intent of a warrant is to convey authority on an individual, allowing them to contractually bind the Government. So based on those references and what I read in the UAI, I agree that the net amount of a modification is the value that should be applied against a warrant threshold. The FAR/DFARS/AFARS don't provide that level of detail.
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So, the correct answer is to defer to USACE for interpretation. The organization issuing your warrant combined with the language they use on the warrant is really the ultimate authority in this situation.