Good question.  Every case is different, but if that is how the prime's normal cost accounting system is set-up then yes they would be entitled to the O/H.

See FAR Table 15-2 (at FAR 15.408) II Cost Elements.  The subcontractors costs are part of Materials and services and they help make up the base that the prime's O/H rates will be applied to in order to calculate the prime's O/H pool (rate=pool/base).  Remember, it takes effort by the prime to manage their subs.

Additional guidance on settling equitable adjustments due to change orders can be found at: 

FAR – Part 43 Contract Modifications
DFARS – 243.204-70 Certification of Requests for Equitable Adjustment
DFARS – 243.205-71 Request for Equitable Adjustment
DFARS PGI 243-204