Although both requirements received a different project number, the requirement for design did not change. Are both designs considered the same requirement? Are design efforts for both projects held to the same 6 percent Fee Limitation or are they two separate and apart Designs with it's own fee limitation?
Have you considered having the original A-E firm perform a redesign at their expense? Your contract with your original A-E contractor should have contained the clause FAR 52.236-22 -- Design Within Funding Limitations. This clause requires the Contractor to promptly advise the Contracting Officer if it finds that the project being designed will exceed or is likely to exceed the funding limitations and it is unable to design a usable facility within the stated funding limitations. Additionally, when bids or proposals for the construction contract are received that exceed the estimated price, the contractor shall perform such redesign and other services as are necessary to permit contract award within the funding limitation. These additional services shall be performed at no increase in the price of this contract. Only if the Contracting Officer finds the unfavorable bids or proposals are the result of conditions beyond its reasonable control of the Contractor shall the contractor be relieved of its responsibility. Remember though that the A-E firm is supposed to be performing a continuous estimate as they are designing so they are aware of what the cost to build is at all times.
This is one requirement and giving it a different project number does not change what is the end project is. Thus the 6% statutory fee limitation would apply to the entire design costs. With that said there are issues you can consider. Lost design is one of these. Has code changed? Is there redesign required?
Lost Design” would be design services which the A-E firm has performed but, because of changes to the project, the design is no longer of any use for the project. For example, a specific control system was originally designed for a project and later determined the control system was too expensive and was deleted. All the design associated with that control system would have been performed by the A-E firm but now to be deleted. That design is no longer valid (because the control system will not be a part of the construction) and is an example of “lost design.” Lost design must be subtracted from the design fees (cost to originally design is subtracted and new design cost is added back) for the purpose of calculating the 6% statutory fee limitation.
If you choose not to hold the original contractor accountable, are you requiring this new A-E to sign and stamp the drawing and be professional liable for the other A-E’s design? You could potentially pay them for reviewing the design for code changes outside the 6% fee.
See DFARS 236.606-70(b)(2) - Statutory fee limitation for specific guidance on redesign and the statutory fee limitation.
Overall, if you have already paid the first A-E the full 6% of the Estimated Construction Cost (ECC), you will have a difficult time finding ways to pay this contractor for his services and maintain the 6% statutory fee limitiation.