I live in a 1950's cape house with a finished attic. The rafters are nominally 2×6. I want to refinish the attic with better insulation and called in a structural engineer to make sure the roof is up to holding the additional weight of insulation and snow load. The verdict was it should be good with some reinforcement. The engineer advised me to a) reinforce each collar tie to rafter connection with a 5/8 in bolt and b) nail 2x's across the rafters along the top plates in the attic and attach the bottoms of the rafters to the 2x's with twist straps. The idea being to have the straps tie the rafters to the joists and do more to keep them from sliding out and my roof pancaking.
I toyed around with a 12 in simpson strong-tie twist strap to see how it fits and I should be able to make it work if I run 2×6's along the top plate. What's giving me pause is that the rafters are toe-nailed to the top plate and the nail heads are are right where the strap would go. 
Is it safe to grind the nail heads flush with the surface? Is it safe to drive more nails that close to the end of a 70 year old what I think is douglas fir rafter? I would pre-drill and only nail through the top 4 holes on the strap but I'm cautious because I've worked with similar lumber elsewhere in the house and it's petrified. Am I misunderstanding what the structural engineer suggested and have this backwards somehow?
Best Answer
Just tap the toenails in deeper. Use a finer tipped chisel if you need to. Then attach it as the engineer has specified.
Even if the wood is rather old, the direction of the force that the nails and bolts are acting in shouldn't rip it apart. It'd be noticable if it was dangerous from your photo and that's not the case.