Wood Flooring repairs and patching

I have begun a remodeling project and removed a wall and two closets in preparation of enlarging the master bedroom. THe floors are typical mid 60s oak hardwood floor planks 5/8" x 3" or so (I think) Anyway the places where the walls were removed have no flooring and I must patch in between with same floor boards salvaged from a foyer tiling project earlier in the year.
The problem is that the salvaged boards have the original nails in them which are set, patched and varnished over on the top and sticking out the unfinished bottom. If I try to nail the board as is or remove the nails the board splinters at the head and will require repatching eventually.
The advice seek is: Would it be better to just push the nails out, flip the board over (unfinished side up) and then nail it with fresh nails in the old holes. I do plan to sand and refinish the whole floor. Will this cause a color variation in the patched areas. Should I stick to installing them finished side up? I could also clip the nails and use adhesive to put them down. Has anyone done this? What were your experiences? What method works?
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There shoudn't be a problem just buying new wood if the nails are giving you problems and you are sanding. Wood is cheaper than time.
Your descrition is not clear. Do you mean 5/16"? or are you talking about 3/4" with a tongue and groove?
Either way, you can pull the nails from the backside with dykes, looks like a flat headed wire cutter.
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