Synce Syntentics are not hollow, you are going to have to find some kind of paint to cover those threads. I would have used a more natural fiber for the sewing, so it could be covered, and colored. Don't feel badly. I used Synthetic " sinew " which is waxed nylon or something like you have, to sew up the holes in my elkskin pants, and to do the seams. I don't regret the seam work, as I did the pants inside out, and the threads don't show, but the patches do. Oh, well, It only took me another 20 years to learn how I could use that mistake to help someone else. I just wish I could have told you before you did the sewing. Its a relatively small hole, so you could pull the thread snd resew it with someting better, or at least not so obvious. Leave the last couple of stitches in place while you run the new threads through the other existing needle holes. When you have most of the patch sewed on again, you can take the rest of the stitches out, and throw the thread away. Leaving the original thread in place will help hold the patch in the same location, so that you can get the holes for the new thead to stay lined up with existing hole in the bag.