Are we required to report negative $ value for the first-tier subcontractors as part of the Service Contract Reporting SCR (FAR 52.204-14)?

seems to me you are required to report the total amount you invoiced the government, not the total amount subcontractors invoiced you. Did you invoice a credit to the government for this subcontractor "refunded" amount during the applicable year? If not, that amount is not reported for the paragraph in question in the regulation. However, you may have some other kind of issue with this "refund" depending on the reason for the refund, your contract type, etc.

Here is the final rule, published in the Federal Register:

https://www.federalregister.gov/documents/2013/12/31/2013-31148/federal-acquisition-regulation-service-contracts-reporting-requirements  

Note that the rule requires total amounts invoiced for and manhours expended by the prime and it’s first tier subs for - services performed during the fiscal year - not necessarily dollar amounts invoiced during the fiscal year. E.G, September services would generally be invoiced in October of the next FY.

The report is to be submitted by Oct 31 of the next FY in order to allow contractors and first tier subs to compile the data.

Since the report doesn’t include lower tier subs, it won’t necessarily represent every MHR expended or dollar invoiced on a service contract.

If a sub didn’t perform any work during the FY, then you don’t report any data for the sub. The amount invoiced is for work performed during the reporting year FY, not for work performed in a previous FY and now corrected.

I suggest verifying all of this with the govt’s contracting office.