So my flooring contractor sanded down my brazillian cherry floors on the first floor and installed new red oak floor on the 2nd floor of our house, we stained them a dark brown almost ebony. Love the color! The problem came in on the final/3rd coat of the Duraseal finish(used this because he said it's best to stand up to our 130# dog). After the 3rd coat dried we noticed white spots sprinkled throughout several rooms. The flooring contractor said the painters must have contaminated the finish between the 2nd and 3rd coats and when he buffed them it spread the contaminant all over the house. the problem is the floors were well covered with red rosen paper and then the painters put their drop clothes over the paper. In addition to the spots there were lap marks every so often, his response was that the Duraseal poly did not flow/spread evenly due to some contaminants still in his pad from when he buffed out 3rd coat. He then tried rebuffing the floors and took them back down to the 2nd coat and reapplied the Duraseal. The white spots are gone now but the finish has more lap marks and a few shiny spots here and there. We met this morning with the rep from the distributor where he bought the Duraseal and the rep said since the floor is so dark Duraseal was probably not the ideal finish to use in the first place, but suggested my flooring contractor screen buff again and then apply matte Bona Traffic HD. He said it will flow easier and is much better suited for very dark floors. He said because it flows easier there will be no lap marks or shine and the finish will be smooth and "I'll love it". My concern is will this actually work? Can I put water based Bona over 3 coats of Duraseal Poly and get a good bond so it doesn't peal later on. It's not horribly noticeable, but the house is very bright and when you look down the hallways you can definitely see the lap marks in the sun. My wife is worried we will end up with a floor in much worse shape if this doesn't work and wants to just live with the imperfections. My take is that we remodeled the whole house and I would prefer everything be done correctly. Neither one of us wants to do a full sand and start over since everything is cleaned and we were about to move in before we had this issue. PLEASE HELP.

Dark brown or black floors reflect like a mirror. A matte finish will reduce the reflection. If you only notice the blemishes in the reflection, I would hope you can accept the job as it is. The floor is protected from wear, now. If you want a piece of art, go for the matte finish. Maybe the contractor figured since it is such a dark stain that it will be a problem to come out perfectly after three coats of finish and can afford to apply another coat. He has done the best he can.
If you would like the Matte finish, paying for the materials would be the least that you could do. This finish is expensive. Have you seen a job he finished with this product?
Too thick of a finish makes it more prone to chipping with hard stress.

Thanks for the reply. I have not seen his work with Bona or a matte finish. I have been using this installer for 10+ years and his work has always been good, this is the first time I have had a problem with him. As for the blemishes in the reflection, yes you see them more in direct sunlight but they are also noticeable at night with the lights on, but much less so. The thing that is most bothersome is that you can see the lap marks and some areas are more shinny than others, the rep from the distributor said the combination of Bona Traffic HD and the matte finish will smooth things out because it flows better than oil poly and won't reflect any imperfections. Is this true? Also I'm just concerned that putting the Bona over 3 coats will peel over time and make this even worse. Should I try the Bona matte finish of live with the way they are, they are not horrible as-is just not perfect or the way they should be. Thanks in advance for you help.

If the directions are followed for the re-coating process the water-based finish will adhere well.
In my experience water-based finish is tougher than poly, but not quite as hard.The water-based finishes scuff a little easier, hence the acceptance of the ul -tra matte finish, so scuffs don't show as much as with a glossier finish. So because of the toughness the water-based finish doesn't wear off, it just scuffs and looses its shine. Abrasion tests demonstrate this like toughness of nylon vs. hardness that wears off, like chalk.
One reason some people like matte is because the coating will not have the plastic look from being shiny and is more "natural".
I always recommend a water-based finish for re-coating a worn floor because it sticks well and seems to last longer, if scuffing is not an issue, like with semi-gloss or even satin.
I think that poly is slipperier, so dogs don't get as much traction and nails slide instead of scuff and don't get the traction to dent as easily.
Just some thoughts, if it would work out I would recommend the coating, if you do get claw dents from the dog they will show up less with the matte finish.
Anyway with a large dog the floor will show wear and not be like new for a very long time.

Bona tech support recommended two weeks curing time for their oil poly, before applying water-based. I imagine Duraseal is similar.

I'd find out if your floor guy is comfortable using Traffic. Not everyone is used to water-based. If he is ok with it, try one test area. You'll be paying for a gallon of Traffic to do this, and it's expensive. At least you'll know, and if you like the look, you can go ahead.

Well we did a coat of the Bona Traffic HD X-tra Matte last Friday over 3 coats of Duraseal and it looks great. Hopefully it will last. Thanks for everyone's help.