Having come across this myself, I had devised a method to correct it but until now, I never documented it, So here is my effort in making an O or zero out of a large dot. If you look, the center of the "O" is not present, I set this up deliberately so I had to follow this through to completion Knowing what I am going to do, I start Softy and load the glyph into the TTF window. Now, in order to make this work, I have to create a inner circle, but since this is to show you, please, It will not be a perfect circle, just a circle detached from the outer circle. What I did here was to add a couple of points to the outer circle by using the POINTS > SPLIT feature and then proceeded to pull these points into the center of the outer circle. I then deleted the point that is circled and pulled the two points that I marked in red together. How you do it really don't matter, just that you do it. I am sure you will find a different way depending on your circumstances.

When you get one exactly over the other you will get this dialog box pop-up and ask you if you want to split contour?, to which I answered yes. This split the two points off the outer circle and I now had the makings of the inner circle

Now, again using the POINTS > SPLIT I added as many points as I thought I would need to make a circle

Now, with as many points as I needed, I adjusted them around to make the inner circle look like a circle. When you are satisfied, you need only to CENTER >UPDATE the glyph and then save it back to disk

Well, you have seen what I started with, this is how it was finished. I hope this is of some help to you. Most of all, have some fun while you use this program. I find it serves my interests and allows me to enjoy what I do with it.