Dear Frank
Only now do you finally tell me that the birth hardwood is Yellow BIRCH hardwood floor. And this is your most major problem. This is one of the most moisture unstable of all the commonly used hardwood floors. So I'm sorry to say your builder choose the worst wood to use in a climate like Ottawa. You are absolutely correct when you say that filler is not wood. All the filler in the world will crack out by one or two years, this is not a solution to a poorly installed and poorly though out species choice.
The best thing would be to remove all the floor and replace it with a more suitable species like maple or oak. If that is not possible For sure have the gaped areas removed and repaired. This may prove difficult, if the same sized wood is installed. The last row will have to be a wider piece ripped to fit. Make sure there is not much if any filler used. A professional floor guy knows how to do this, without using filler. Oh, and make sure that the whole floor is not stapled down, they should have used flooring nails. Make sure they do not try gluing the repair wood to the subfloor. These staples will continue to cause problems throughout the life of the floor. If your contractor doubts this, I have the university study on this. Also an OSB subfloor has the tendency to shift more than plywood, and a very thin 5/8" osb subfloor will hold the floor nails very badly indeed. Again I can back this up with the studies.
Next, if they intend to sand the floor after the repairs, that's fine. But the whole floor must be sanded professionally 3 times and no visible edger marks should remain. And they must now apply 3 coats of oil modified polyurethane. NO LACQUER SEALERS !!!!!! Due to the builders poor choice of wood, this is the finish needed to keep the wood more moisture stable. They will be removing about 1/6 of the total life of the floor. The builder will need to compensate you for the removal of the wood, and vacating the house while this harmful wood dust is made. You see this may be a lot more costly than either you or the builder thinks. I have won three small claims court cases against contractors, so I know that he is responsible.
All this said and you still need to do your part and keep the house humidified. If you fail to pay attention to all I said in my first email, all the rest I have said is also void. Get that hygrometer, and don't do the repairs until the spring. When you order that hygrometer be sure to tell esci.com that I sent you, it's the best buy I could find for a really effective instrument.
Oh, and be sure to dehumidify the basement once the spring begins. Let me know tonight what you think about this.
As always your Most humble servant, Joseph, the Wood Floor Doctor.