So many difficult concerns with the thread on these appliques. I would be most concerned about the strength of the threads. The need to check and see if the thread is worn using a toothpick is a good option. It the thread is worn out then re-stitching the entire quilt may be the healthiest way to restore it. Removing the old stitching and reworking the entire quilt will be time consuming to say the very least. The best option in my opinion is to leave the coloring as it is if that is the only problem. I see it as a distinct character of the blocks and the quilt maker and needs no change to make it all black. No matter it will be a beautiful quilt.