Wood – It there a easy way to handle floor cupping

There is really only one way to rid yourselves of the "white" fill spots. You will need to carefully dig out a small amount of the filler so only dark wood is showing around the edges. You don't need to remove all the filler from the original hole. Buy a pre-colored filler crayon, Minwax and others make them. Match the color of the filler stick to your floor color. Sand a small area around your repair with fine sandpaper, an inch or two is plenty. Fill the indent with the matching colored filler, smooth it well and put a couple of coats of urethane over the repair, feathering the urethane into the existing urethane finish. A foam brush would be good for this purpose. Good luck.

@iLikeDirt covered a lot of important information, but I'd like to add something since the majority of the information assumes that there is a problem of excess moisture due to the concrete, while the expert assessment says it is actually dry cupping that is the problem.

Dry cupping implies that the interior humidity is dropping below the average frequently enough that the wood surface dries out. It sounds like they are suggesting that the vapor barrier between the slab and floor is probably doing its job correctly.

One way to help prevent this is to bring the wood into house and allow it to be exposed to the air within the home so the moisture content is similar to that within the home (acclimation). I like to assume this is standard practice and this was already done, but if you're using a special reclaimed antique pine wood, then maybe a longer period would have been desirable. Major seasonal humidity variation can still have an impact.

Do you know if there is a period during the year where it seems more prominent, or has it not been long enough? If I had to guess, it could be during the summer when the AC/dehumidifier is running more frequently. I'm not as familiar with the climate there, but in parts with cold winters you are more likely to encounter dry air issues during the cold months.

One thing that could be happening is that the glue on the underside of the wood is acting as a seal on just that side, inhibiting the wood from 'breathing' underneath. The only surface area for moisture to leave the wood is on top. A solution that allows the wood to better breath on the bottom, or simply avoids using glue or too much glue, might help. But then you need make sure the vapor barrier is doing its job or you will end up back where you started with too much moisture underneath, the expert seems to imply you no longer have that issue though.

You can still end up with this problem with engineered floors. It could still be a problem with an unknown source of moisture throwing things out of balance as well. I'd see what the neighbors are doing as a solution for your area and if they have similar problems before I spend more money.