Let me preface this by advising that I run a hardwood flooring company with a partner (and I am the partner that does not refinish, my contributions are more in the business sense in the office versus flooring out in the field). I am always trying to learn all I can about the trade. My question is this: I'm was told that with regard to engineered hardwood floors, pre-existing oxidation is not ALWAYS visible prior to sanding/staining. Is it possible to not be apparent before sanding/staining and then appearing after refinishing? If yes, what causes this and why would it not be visible until after staining? The floor at issue is engineered oak, had no visible signs of oxidation until after applying the stain, and then 6 perfectly spaced dark spots appeared in front of a large window.

You may be referring to oxidation caused by sunlight. Strong light will oxidize some of the color pigments in wood. If the floor was subjected to strong light, with any object sitting on the floor to block light penetration, the object(s) will leave a photograph of the outline of their shape.
If you inspect the floor before sanding, you should be able to notice it. It will show through the stain. Windows and skylights are hard on wood floors.

Pete A. No not referring to oxidation caused by sunlight. The oxidation was invisible to the eye, maybe caused by plants (loosely circular shaped areas, each about 10 - 14 inches wide and equally spaced about 3 feet apart) along the front of a window. The oxidation (engineered floor) was not visible or apparent until after sanding and staining. Follow-up blending, feathering, additional coat, nothing made improvement. They did water pop the eng floor, maybe that had a contributing factor. The spacing of the spots are too deliberate to be random.