Sinus Discomfort Post-blephroplasty - Will It Go Away?

Anatomically, the sinuses are far away from the eyelids and the areas, where eyelid surgery is performed. Either, your pain just appears to originate from the sinuses but it is really related to the eyelids. Alternatively, your sinus discomfort (and most likely you are referring to the maxillary or "cheek bone" sinus) gives you trouble as a coincidence.

You should mention it to your blepharoplasty surgeon and follow his advice.

Sinus discomfort should have nothing to do with your blepharoplasty.  I would suggest you see your primary care physician and request a sinus xray.