If the subcontractor's position is still above our disclosed evaluated position, are our counteroffers considered to be certified cost or pricing data?
Your counter offer to a subcontractor is considered certified cost or pricing data (CCPD) only if it supports a figure in your proposal. I presume your price proposal reflects a higher figure and you've supported that higher amount with the initial subcontractor quote. This is generally a poor negotiation tactic unless you are truly acting in good faith.
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I'll bypass detailed comments on the integrity of the CCPD flow-down clauses, FAR 52.215-10 and -12. But know, that ACO's and Auditors are aware that contractors can stall their subcontract negotiations until after they submit their CCPD certificate to the government. Where a pattern of this behavior develops, Contracting Officers can rightly use DFARS PGI 215.404-3 to justify applying a decrement to the subcontracting portion of your proposal during negotiations. This can easily sour the environment before work even begins!
The sole source RFP that you are proposing against contains the provision at FAR 52.215-20. Paragraph (b)(1) in that provision states that Table 15-2 should be treated as if it were incorporated into the text. This gives authority to "Note 1" within Table 15-2, which says the requirement for CCPD continues up to the time or agreement on price and updates should be submitted promptly. Paragraph B of Table 15-2 indicates that you must annotate, on an index submitted with your proposal, subsequent changes to your CCPD all the way through the agreement on price.