I have to agree that these were preexisting but almost invisible because of the sanding. The top pic looks like "old finish" was left in place. Considering how thin your boards are and how old they are, this is not unexpected. And to be clear, old floors can have 80 years worth of contamination (ie. wax, shoe polish, Pledge, Murphy's Oil soap, soap, hairspray, hair dye, etc) on them. These products can, and will, get past the original finish and contaminate the wood. Just like old urine stains pushing all the way through a board (the dark gray stain is most like an old urine stain...cause that's what they look like after many years), these contaminants can go several millimeters into the wood. Especially things like cooking oil, Murphy's Oil soap (anything oil based really) or even melted wax from a candle. After sanding, you wouldn't have 'seen' these things. But a quick swish of a slightly damp mop (make it wet to give some depth of colour) and all of these things would have been evident within moments of the water touching the wood. And that's why you can see them now. The clear coat is like water hitting the wood. It gives the colours depth...and definition. But unlike water, the finish is permanent. At this point, I would keep going with your plan = 2 more coats of Loba 2K Invisible. And You will want to hurry. To get a good 'stick' the next coat should be put down within 24 hours of the previous...or else the flooring guy has to abrade the floor again to get a mechanical grip rather than a chemical stick. Keep going. Know that you are getting 20 years more out of these floors that probably should have given up the ghost 20 years ago. That means you are extending the life by 40 years. For an old hardwood floor, that's impressive.

@Chelsea Ivers I have only done door panels on sides of boxes, and they turned out reasonably well, but I am still having problems perfecting my finishing method. The doors and drawer fronts will be the next things I tackle. My latest issue is pock marks, otherwise known as fisheyes, that I think are appearing due to excessive humidity. I have created an enclosed painting booth that tends to trap vapor as it evaporates from the coating, and during a rainy week here where I live, I could not control the pock marks appearing in all layers of Loba 2K Supra AT even with opening a couple of windows that adjoin the booth. The WS EasyPrime did not have this issue, but again, that was the first layer, and successive coats in the 4-coat system released more humidity into the air. Other things can cause fisheyes like excessively thick coats or improper temperatures of the air and substrates, but I believe in my case it is humidity and will be trying to address this going forward with a robust dehumidifier inside the painting booth. I would be happy to personally speak to you about the process, but it would really be better if you started your own thread and posted questions there so that everyone searching for Loba application information in the future could benefit. Alternately, I just switched my settings over to allow you to be able to message me privately, but if I don't hear from you, I'll be switching that back off by the end of January 2021. You should be nervous, actually! This is a terrible coating to apply on cabinetry, and I highly encourage you to select a different finish! I'm in the middle of a project so already committed, but many times during the 16 coats I have already done with 6 to 8 hours of prep for each coat (with the exception of the hot coat of Supra 1 hour after primer) and at least half of the work left to go for a small kitchen, I have regretted ever signing up for this monumental task. If you haven't read my other thread on Loba for cabinetry and followed the links within the posts there, it would be of benefit to you: https://www.houzz.com/discussions/5927222/loba-2k-supra-a-t-coating-questions#n=26 If you haven't yet purchased your Loba products, please visit the Envirolak website and check out their clear coat finishes. Envirolak would be much more suited to a cabinetry application. Envirolak is based in Canada and is gaining a solid reputation for robust, one-part waterborne coatings, including clear coats, that are created to be brushed and rolled on. If you don't have a dealer near you, you may contact Envirolak directly, and they'll be able to work with you to get their products. This would be the next-best thing in durability to a catalyzed 2K (two-part) finish such as the Loba 2K Supra A.T. Another alternative would be General Finishes. They do some beautiful one-part waterborne clear coats that are probably not as resilient as Envirolak's but are easy to apply with brush and roller, and many people who have posted in the Houzz forum have used General Finishes to satisfactorily coat their cabinetry projects. Here is one thread with more information about that: https://www.houzz.com/discussions/5633128/most-natural-matte-satin-finish-white-oak-cabinets#n=33 One of the first problems you will encounter with Loba 2K Supra A.T., or indeed any of Loba's 2K coatings, is that they begin to set up at lightning speed. You must lay the coating down and walk off and leave it within no more than 10 minutes per piece, and really more like 3 minutes per each section of each piece. The learning curve is steep, and I'm still having problems getting my coating to lay down without brush marks as the quick drying occurs. Another problem you will encounter with Loba's products is that they are formulated with no vertical hang properties. All the leveling properties are horizontally self-leveling. So, any time you have something other than a perfectly flat surface, the Loba coating will drip, run, or puddle. I have created a complex system of taping off low-lying areas, then wiping the puddles with a microfiber cloth, then removing the tape with care not to drip onto finished sections, then painting the previously taped areas, then sponging off more puddles, then wiping out more puddles with craft swabs. This all happens within seconds as I move quickly with no wasted motion as the coating is already flash drying in surrounding areas. The process is difficult, stressful, and not entirely successful as I have many surface blemishes throughout the project thus far. I have had to coat each plane separately using several rounds of Frog Tape with plastic draping to mask off non-working sides. Please, if you have any other options, go with the other options. The best thing would be to order prefinished cabinetry or to have a professional spray the project with Milesi or Renner. You may learn more about professional spraying options at this group: https://www.facebook.com/groups/diycabinetrefinishing The Loba 2K Supra A.T. with a 4-coat system including WS EasyPrime primer as the first coat is basically impervious. You'll never be able to refinish your cabinetry pieces unless they are flat surfaces that can be mechanically sanded. It's that tough. You may even have a hard time hand sanding between layers prior to full cure due to the incredible resilience. It's like dipping everything in plastic. The finish is beautiful, but I think in most cases that the durability is overkill for cabinetry. Loba's 2K products are designed to last 20 years on a flooring surface that you walk on during those decades. The Envirolak or General Finishes one-part waterborne products should give you plenty of years of wear without the headache of dealing with 2K application concerns. I hope this is helpful to you. If you would like to start a new thread with your own project and photos, please be sure to link it back here so we can follow and comment on your new thread.

Thank you so much! I appreciate the expert advice. I'm definitely not an expert! I think I used the wrong term earlier - when I said 'raw'. What I meant is that that ideally the colour looks like natural wood, as close to white oak as possible - vs. something that turns pink, yellow or orange. We do want some shine, and are leaning toward a satin finish. So, in that case, would you still recommend Loba invisible? Concerned about durability, as we don't want to be fretting about the floors. These floors are rather yellow, which is why I asked about the UV blocker or stain. Edited to add: we also have the option of delaying this work and waiting until someone that can do both Bona and Loba is available. So, if Bona might be a better option, that's something we can consider. Quite possible I'm overthinking this ;)

Isn't this a duplicate post?