A.Michael Purser, a second-generation wood-flooring contractor in Atlanta, responds: Color variation is common when new material is used to patch a damaged inlay or section of flooring. (For example, recently milled mahogany will be lighter in color than the older, original material.) So I always make a special effort to match the patch with the original. Depending on how accurate the restoration has to be, I look for new wood that's the same species, the same milling — that is, quarter-sawn or flat-sawn — and the same age as the existing floor. Suppliers of recycled lumber are a good source for this.
Also, don't plan on staining the entire floor to "even out" the finish. Old floors typically weren't stained originally, and doing so now will only obscure the contrast between different species of wood. There will be a color change when the floor is refinished, of course, due to the loss of the very top layer of wood — darkened from UV exposure...
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