After an anti-squeak effort, we've got a bunch of 1/8" holes in the hardwood floor. These are aligned with the original nail holes, so they will blend in if darker than the wood.
What putty should we use? After that do we apply a little dot of polyurethane? Sand? I spent some time at the hardware store, but none of the putty or products mentioned floors as an application. The existing floor appears to be a semi-gloss, but I can't be sure (it was refinished prior to our home purchase, but the contractors did not leave any stain or supplies). I'm more concerned about feathering the poly layer, compared to matching the color.
My floors have 8mm of hardwood, 1mm of paper spacer, on top of 18mm of old growth Douglass Fir boards. The house was built in 1938, and everything is obviously stabilized from a moisture point of view. The floors bow slightly as the beams below are overspanned.

