This is a pic I found online, which I found to be true when doing some samples on my red oak floor. If you want water based you might want to stain first or add a tint vs just the poly on oak. Oil mellows some vs water based will not change in color. Here is a link that might be useful: pic

What Couture wrote.. Water based finish can pop the grain on wood causing it to be rough. A screen can leave swirl scratches so we generally use an abrasive pad with a couple of strip of 150 grit sandpaper strips stuck to the surface. in the absence of the adhesive sandpaper strips, sticky back orbital paper can be used. Or one can buff with a screen disc then follow up with the abrasive nylon pad.

Polyurethane is not water proof. It is water resistant but not water proof. It will slow down the transition of water from the surface into the wood but it won't stop it completely. My guess is the edges that allowed a snick more water to reach the wood have had a snick more finish taken off. That's about as exciting as it gets. The drop in the gloss level is not something I would worry about. You sanded a finished surface. In other words you scuffed it up so much that you reduced the gloss level. Have you removed all the finish? No. Have you reduced the gloss level? Yes of course you did. That's what sanding does. Again, the issue with adhesion is going to be an on-going situation. Regardless of gloss loss or not. You can test treat a plank or two and leave them alone for 2 weeks (allow full cure) and then try the scratch test. I would leave them alone. Install the floor and use it until it becomes so bad that a full sand/refinish is needed. The only way to ensure good adhesion is to do a full sand/refinish. Until you get to that point, you could be setting yourself up for failure.

The 2part water based products in the middle to high-end range (more than $130/gallon) will out perform your every-day oil based finish. To get the toughest finish for your budget, I like to see 3 coats of whatever you are working with. The two-coat system often requires a 'buff and recoat' by year 15 (some people need it done by year 11 or 12). If you go with the three coat system RIGHT AWAY then you can skip this step in the future. The benefits to water based: They are clear and colourless and do NOT turn yellow. They have a very fast 'cure time' of 7-10 days. They are (normally) low odour which is a great benefit to those of us who have chemical sensitivities, asthma, COPD, migraines, history of nose bleeds, etc. The down side to OIL based: They turn orange rather quickly (within a few months) and they get darker and darker as they age. They take a LONG time to cure (full hardness = full toughness) like 30+ days. The ODOUR is one of the greatest drawbacks to oil based. For some, they can 'handle' living on the same level of the floors within 2 weeks. Whereas others (I'm included) cannot live in any part of the house until 4 weeks has passed.