Hello I just became a new member. I figured this was the best place to come for advice. I have been building an addition on my house which is our master bed and bath. Fortunately I have a good friend in the timber frame business so we went with a post and beam set up. This has unfortunately been a year long project working whenever I can on the weekends. I live on a farm in Virginia and two years ago I had an American Chestnut barn fall down. I ended up getting it milled into flooring. It is some good looking stuff with a lot of knot holes and worm holes. My question is what it the best thing to fill the holes with before sanding. I am big on character so the imperfections are what I am looking for. But I also want a smooth finish if possible. Excited about being a part of y'all and hopefully I can get some good feedback from y'all.

I have never seen a Chestnut floor,but I can imagine a beautiful brown color.I hav e installed antique pine flooring that had bolt/nail holes along with nail holes and staining. The large knots weren't always intact. I have filled holes with epoxy mixed with sanding dust from the edger that is from 80 grit paper or finer. Any all purpose epoxy mixed with about twice as much dust by volume will make a peanut butter/putty mix that will fill large holes without shrinking. If it is too runny you add more sanding dust. You will be laying over a sub-floor that may have kraft paper over it as a moisture barrier. This will be a little darker color than the freshly sanded wood and look more like a knot and blend in without looking trashy.
If you would like to have a black filler that matches the iron stain that comes from rusty nails, you could use Bondo type polyester filler that is colored with lamp black. I think that it can look grey instead of black and stand out too much.
Make some samples if you use Bondo that are finished like you are planning to finish your floor.
You have a treasure!

Kinda disappointed in the response that I am getting. I guess there isn't a good answer to my question.

You can always sand and apply the first coat of finish of your choice and then putty the areas that you want. You can buy putty already colored or mix your own color. The drawback to putty is that it will remain soft until it cures, or at least forms a skin on the surface. This is why I recommend epoxy or Bondo. No matter how deep of an imperfection/ hole you have the filler will be ready to finish sanding after it has hardened, which may take overnight with epoxy.
Sometimes a colored wood patch can fill installation type nail holes like the face nailing on starter rows or when changing direction. This would be sanded smooth like the epoxy or Bondo before the first coat of finish.
What are you planning to seal the floor with after sanding?