After patching and then sanding the stain will be just a little off. But as far as the finishes go if it was an oil based use that if water use that. But a tip would be to buff n coat everything which will help blend the repair to the rest of the floor

Thanks for the help. I am pretty sure it was oil based finish since it was
The toxic Swedish finish. (Is there one that is water based?)
We realize the best thing would be to blend it in by doing the entire area but it is our kitchen and the floors runs throughout three rooms with no ends. So we will just have to sand and stain that area. See pic

Swedish finish is generally how one refers to an acid curing finish. Oil poly is generally how one refers to oil-modified polyurethane.
The difference between the two is significant. Acid curing finish smells much worse and is harder to use. The main VOC component in oil-modified polyurethane is mineral spirits, which is not particularly toxic (http://en.wikipedia.org/wiki/White_spirit) but it does smell and dries slowly.

Ideally you could find the person who did the work and pay him to finish the patch, but even then, a perfect outcome isn't going to happen.
If you're going to DIY, you're probably better off using oil poly. Water-borne urethanes are readily available and have lower odor and toxicity but will be less likely to duplicate the look of the existing finish and good ones cost more that the oil poly.

If you get the color right, and get close to the sheen, very few people will notice it.

Especially if you put some furniture in that area.