This response is based on the information provided.  We suggest you discuss with your contracting team, program manager and/or legal department as appropriate. 

We will restate the question as we understand it and you will be able to determine if we are answering the question you intended to ask.

A contractor was awarded a contract and submitted cost or pricing data using its cost model.  It is now submitting cost or pricing data for a modification to that contract.  The change, taking the absolute value of additions and deletions into account, is less than the Truth in Negotiations threshold of $2 million.  However the contractor added the change to its previously submitted cost or pricing data.

The key question is whether or not you can segregate for analysis purposes the cost or pricing data for the proposed change from the initial submission.  If you cannot do that, you should have the contractor submit cost or pricing data that stands on its own and can be analyzed for the new/deleted work.

In any case, the submitted cost or pricing data under $2 million doesn't meet the certification threshold.  FAR 15.403-4()(1)(iii) is useful on this subject.