I'm going to answer my own question for anyone who is having a similar problem. We are going to use a Pre Finish Flooring Wood Filler. They are meant for touching up pre finished floors (both factory finished, and ones that were finished on site). A bunch of companies make them; we're going with Wood Wise. They come in a bunch of colors, and you can mix the colors to get a closer match. I learned about pre finished floor wood filler on the internet and our hardwood floor installer confirmed that it is the right product to use. :)

This is only my 2nd post. I so appreciate this forum and all I'm learning. Everyone is so helpful and I'm amazed at the wealth of knowledge and experience among all of you. We are planning a remodel of a home we just moved into that hasn't been touched since it was built nearly 30 years ago! WOW! It was a spec home in 1981 and most everything is "builder's grade." The kitchen is atrocious to say the least. You can imagine how dated and worn out it is. What a challenge to make all the changes necessary within a budget. Anyway, I do have some food for thought on this subject. For the past 12 years I had oak floors in the kitchen of my 1930s Acadian cottage in southeast Louisiana. The kitchen was an addition so we matched the floors in the original house and they were nail down & site finished. My children were young teenagers at the time and very active. We did take our shoes off (all of us) inside the house to help protect the floors, but other than that we did nothing special to baby them. When necessary in the kitchen I only spot cleaned the floor with a damp rag and I would immediately dry it with a soft cloth. I always wiped up spills or dropped ice cubes immediately. I found the floors in the kitchen (and the rest of the house) very beautiful, comfortable to walk on and easy to take care of. We had no problems at all in 12 years. When we sold the house last month there was not even a scratch anywhere throughout the house. In my opinion they looked as good as the day we put them in. That said, there was a day disaster might have struck. I just so happened to be at home when the pipe to the kitchen sink sprung a leak and it was not a drip....but a trickle. I was able to use lots of bath towels to keep up with the leak until help arrived to fix the problem. There was no swelling to the sink cabinet (it was all wood) or the flooring. But, I know if I had not been home and the leak had continued unchecked for hours it would have been a disaster for the floor. Due to that experience alone I may have a tile floor in the kitchen at this house. Then again...I just loved my wood floors in the kitchen! :-)

Well, I'm finally checking back on this thread. We just moved back into the house after having the new wood floors installed and then having the old and new floors all finished at the same time. DH would not budge on the finish, so we ended up with the Swedish Oil Finish. I mentioned to DH that some states have made Swedish Oil Finish illegal, but he still wanted that finish for our floors because that's what we had before (or so the guy who bid the job thought). Want to know something funny? The day before they started finishing the floors the guys working in our home stated that we had WATER based finish. So who knows? On the plus side, I'm very happy with the looks of our floors. They did an excellent job threading in new boards with the old to combine the new wood floors with the ones that were installed twenty years ago. You can't tell which is old and which is new---it all just looks like a beautiful new floor. We decided to go with the natural finish, and I couldn't be happier. We stayed in a hotel one day longer than the floor guys suggested, and I'm glad we did. Yesterday I spent much of the time parked in the car in front of our house, after DH had gone in (with a respirator on) and opened windows everywhere to start airing the house out. Later, we added fans and then the started the furnace on fan only. As I write this, I'm sitting in my house with fans running everywhere and almost every window open (on three floors). My eyes sting a little and my throat hurts; I have a nagging headache. I also have noticed some impact on my breathing. However, I'm hanging in there and haven't had a full-blown major asthma attack so far. Upstairs is definitely better than downstairs. I'm disappointed to have to deal with this, but it does seem to be getting better. I'm hoping to be able to sleep upstairs tonight, but if I can't, I'm going to ask my sister if I can sleep on her sofa tonight. Does anyone have information on the time it takes for the floor to fully cure (and, thus, for the off-gassing to end)? Also, I'm wondering about moving furniture back in. I've heard everything from two weeks to sixty days, so I'm not sure what to expect. The foor guys seem to only state that the vast majority of the chemicals are off-gassed in the first forty-eight hourss. That's all well and good, but with something this strong, the few remaining can be pretty significant. If I can get through this without a trip to the doctor/hospital, it will be worth it. I'm so excited to finally have this done.

Hello to everybody still following along with this! We finally did get the inspection report back - it was a very through, detailed report. To make a long story short, the inspector found issues with everything: installation of the floors/railings/balusters, staining, the flooring product itself, etc. He addressed every concern that we had, and even found additional issues. I shared the inspection report with the flooring company who installed the floors and stairs, and they have agreed to remove and replace everything. Once we gave them the inspection report, the flooring company has been really great about wanting to make everything right, and making sure that we get a really nice floor/staircase/railing system. They assured us that not a single person who worked on our project initially will be working on it this time. In fact, all of the people who originally worked on our project were either let go, or left the company on their own. Since there were also so many issues with the flooring product and the gray color, we actually decided to go with a completely different brand, color, and species of wood. Our next step is to decide on a schedule for the work - so I'm sure it'll be a while until everything is completed. Thank you to everybody who commented on this thread with your ideas, suggestions, and comments!!!