bypass graft and endarterectomy

Our physician did a right femoral-to popliteal bypass with gore-tex graft (35656) and a right common femoral artery endarterectomy (35371) in the same operative session. We use code correct in our computer system which is the CCI edits, and it doesn't show any bundling issue with these 2 codes. The claim was submitted to Blue Shield of Massachusetts, and they have denied code 35371, indicating it's included in the other procedure. I sent the claim to appeal with the operative report and the printout from code correct showing no bundling issues. Blue Shield has denied my appeal, they use McKesson Claim check, clear claim connection, which shows this is bundled, but if a modifier 59 is added to 35371 it then shows it's allowed.
I'm not sure what to do with this, should these 2 codes be paid and I should add modifier 59 and appeal again? I don't understand why one claim checking system shows them bundled and one doesn't. Can you help me with this? Thank you.