Is "the contractor" also the person who installed the hand scraped? Hand scraped is not going to look as 'finished' as traditional finished flooring; it's supposed to look a little rough. Did your contractor show you samples of what your floor might look like finished? Even smooth floors can look funny and incomplete before the final coat.

Thank you for your responses. The floor guy will be applying three coats of satin finish water based poly. Floors are white oak, if we use Dark Walnut with some small amount of English Chestnut might that give the warmth? Dura Seal makes a coffee brown that looks like it has character? mini wax Jacobean? any thoughts on these stains or other suggestions. I've picked cabinets, fixtures, etc. based on leaving the dark woodwork and when new floor and existing floors are done having something similar to what we have now.

Spot repair using polyurethane is problematic since the finish does not 'feather' well. That means the finish does not blend with existing surfaces in a repair area easily. So, what I have successfully done on several occasions is to start with 100 grit paper(I favor a random orbit sander) and get the big problem areas smooth and chip/flake free. Don't worry about defined edges, just get the problem spots.The random orbit sander is much faster than a 1/4 sheet sander. Then switch to 150 grit paper and get the sanded surface smooth. You want to use the same type poly as when you refinished. Use a rag dampened with paint thinner(if you are using oil based poly finish) or water(for water based poly) and remove all the dust/etc. Apply the poly on the sanded area, using only enough to cover the sanded area. For that small area, a paint roller with a thin nap(thicker naps will cause bubbles)---1/4" nap is fine. Now for the blending/feathering. I use a cotton Tshirt as the feathering tool. I use a piece about 12" square or 6" wide and 12" long. I fold it until it makes a ball with a smooth surface. I dip it in poly and begin wiping the edge of the fresh poly in a circular motion, moving outward until the pad is dry. Then move back into the fresh poly and keep up the blending until the entire perimeter is done. You do not need a lot of pressure. And you will find the best method of wiping as you proceed. Since you will need three coats of poly to complete the repair, you will be able to lightly hand sand the perimeter before another coat.

Oil based soap (like Murphy's) is a super no-no. You then added a polish. Again another no-no. You need to STRIP (chemically and mechanically) the floors of the soap and the polish. Rubbing Alcohol works wonders. Try a test patch. Work in a well ventilated area. Get on hands and knees with the alcohol and a putty knife as your scraper. You will do this for the entire floor. And hopefully you will never need to refinish these floors. Those two products you have applied have drastically reduced your ability to do a full sand and refinish or even a buff and coat later in life.