It's not clear why there would be ammonia in a cloth diaper... or whether the damage is in the finish, the wood fibers below the finish, or both. Ammonia darkening can sometimes be bleached out with oxalic acid. Dissolve the crystals, brush onto the entire surface (not just the stain, because it may lighten the area). When the bleaching is complete, sponge off the bleach with a solution of baking soda and water (to neutralize the acid). If it's urine in the diaper and you're assuming the ammonia comes from that, realize that it may be impossible to fix; professionals usually remove and replace urine-stained boards, at least for pet stains. Even sanding through often won't remove them.

Poly does not touch up at all well. The entire floor will need to be sanded and recoated, and you will still see the line where you stopped at the threshold. In addition, some of these paint remover products or floor cleaning products that you have used will impair adhesion of the new to the old. If that happens, it may look OK at first, but then start peeling off in a couple of months. If that happens, the only recourse will be to sand to bare wood and start over completely. If you've ever used anything with silicone or orange oil in in on the floors, skip the intermediate peeling step and sand down to bare wood now.

The finish has been compromised and you are looking at raw wood. You will need to have this fixed sooner rather than later (you have a few months to do it). Whether you need a full sand and refinish or spot patching, will be up to the professional flooring refinisher and what s/he sees throughout the REST of the floor. For instance, if 90% of the floor is in AMAZING SHAPE (because it was refinished only 5-7 years ago), then a spot-fix is the option you want to look at. If 90% of the floor is in less than decent shape (because the finish is more than 15 years old and it is coming up on it's required sand/refinish event) then the spot finish isn't ideal - in fact it could be a waste of money. I can't tell how the rest of the floor looks, but by the photos it looks a little dry or "thin". When was the last time the floor had a full sand and refinish? Was it 7 years ago, 17 years ago or 27 years ago? Somewhere in your answer will tell you which is the best way to go.

That's a foot print in the stain not just in the finish. Yes the 'fix' is to to a patch repair. They would sand down the area to raw wood, restain that area and then apply 2 coats of finish (with all the appropriate cure times to be observed). Then the entire floor gets a final coat of finish. It is the FINAL coat that offers the continuous finish/gloss level. To reduce your fears, Satin is a VERY forgiving finish. It has a lovely glow. This glow DULLS DOWN as it ages. It might start off as a HIGHER GLOSS Satin (be prepared) but it will ALWAYS settle down. This takes 1-3 months. So don't panic if you see a nice glowy floor on day 1. That will change. Once the 3 months has passed, the floor will sit happily at the satin level it was destined to be. Then, like all floors, it slowly dulls down withe wear. Higher traffic areas dull a little faster. So your foot print area (being in a high traffic spot) will mostly likely dull down nicely. The question becomes: Which bugs you more? A foot print such as the one you found (noticeable once you know it's there) or a *possible* sheen difference that will disappear with age? There is only one person who can answer that question - and that's you. Permanent foot print vs. 'disappearing' gloss difference? I'm not worried about the gloss level. I would worry about the stain variation.