You have "wear through" which is when the finish is pierced and the wood is exposed to the elements. The dark areas are where dirk/water/mud have stained the floor. It is possible to get this out... but probably not all the way. A floor that has wear through needs to be sanded right down, stained (if you wish) and then refinished. Patching can occur...but it is almost always a waste of time because the "look" can be very different from the original sitting right next to it. I don't recommend it for your situation. The second photo shows the deep scratching. Ideally, you would have had your floors looked after BEFORE wear-through occurs. There are some "regular" scratches to the Left in photo 2. You can see it is visible...but no discolouration....THAT is where you draw the line. The darker "wear through" to the Right in photo 2 = too late = full sand and refinish. If you catch it BEFORE wear-through, you can do a "buff and coat". This is a light sanding with a few coats of high end finish over top. The buff and coat is roughly half the price (in Canada at least) as a full sand/refinish. For this reason it is important to catch the floors before you get to this level of scratching.. That being said, you now get to pick some stains (test patch, test patch, test patch). The first photo shows two different woods...you could ask to see if the lighter would could be matched to the darker wood (lots of testing to achieve this). It won't be pefect...but then again you wouldn't have used reclaimed building materials if you were after "perfect". The match can lessen the colour variation to a more manageable (design wise) level. As for "good for dogs" - natural colour of wood = best colour for scratches. A lower gloss (like a satin) can help. You can ask for the "best" finish with scratch resistance that comes in a can. You will pay a premium for it...but it could/should save you thousands of dollars over the long run. A highend, scratch resistant finish means you can get away with the cheaper buff and coats (every 7-12 years...or so) and be able to retain the original (expensive) finish for the full 25 years. The other thing to note: dogs claws require trimming 2-4 PER MONTH when working with hardwoods. This is what the hardwood flooring refers to as "routine" trimming. Some of my clients thought "2-3 PER YEAR" was "routine". I laughed. You have heavy, high energy, powerful dogs. A single lab can cause some damage over time. Two labs can do a number on a floor. Three labs and you have a very short lived hardwood finish. You have 7. I would find the most expensive, scratch resistant finish available in Australia. I would have the maximum amount of finished put your floors (you will pay extra) it and I would budget for a "buff and coat" every 5-7 years.

Thanks for all the great ideas everyone and sorry I didn't explain the polycarbonate a bit better :) This is along the lines of what we'll be using... http://www.psp.co.nz/building-brands/corrugated-sheeting/suntuf-polycarbonate The area is an absolute sun trap and we're hoping to use it as an extension to our living space, especially on rainy days! I've just sent my husband out to get a few pots of different stains for is to try - darkest brown (cedar) and a lighter brown (rustic oak) both by Cabots + the black we already have. Hopefully we can decide between one of those! I probably should have mentioned we will have black aluminium pool fencing running along the top of the second retaining wall - so the real question is do we keep everything black (pool fencing, horizontal fence, retaining walls and pergola) or do we go with a dark (or even light) brown for the pergola and retaining walls.... We just keep going around in circles at the moment. Decisions, decisions! Thanks again :)

Get the professional sander guys in to repair the living areas and kitchen but don't go too dark with the stain as it will kill the lovely grain in the matai. I'm thinking a couple of tones richer than the timber knots showing in your photo, definitely no yellow tone at all. In NZ stepping on to carpet especially in a kiwi winter is so much nicer than a cold floor board shock!!! A nice area rug for the lounge and you're done.

In the areas that need sanitizing... like our nursery... we are using HDPE on the walls. The plywood walls are for other areas, including the training room that will just get normal dog dirt. We don't have kennels in our building.