We have recently built a new house and have been living in it for just over 6 months now. The entire house has Jatoba floors that were finished on-site. We noticed when we first moved in that the filler in the floors seemed really light compared to the floors, and now it is getting even more noticeable as the floors darken. The filler is an extremely light beige colour so our floors are starting to look very striped and all the nail holes and places where the floor had little damages is extremely noticeable! What can be done to correct this problem? There are also numerous hairs that got stuck in the floors during the finishing but we were told that these would just work themselves out -- is this true? Any help would be greatly appreciated.

The finisher used the wrong filler when filling the floors. They do make a B. Cherry ( jatoba ) colored filler. I've used it. One option ( outside of a complete refinish and removal of the existing filler ) is to carefully color the existing filler with an ink touch up felt tip pen. I've used these in the past to repair small problems ( not that yours is small ) and they can work. You may need a "screen and recoat " as well.

The house is 4000 sq feet with everything except the bathrooms in the jatoba flooring. I'm assuming this would be too much for a touch up pen? How would they go about removing the filler if they were to refinish all of them?