I didn't see the same problem, but a less serious variation. My solution was to put the smaller ellipse into its own layer, on top of the bigger ellipse.
But the idea, then, is to remove the crescent in order to have the ellipse slighty flattened... So, I have to have two entities in the same layer....
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I see, I hadn't noticed you were only changing one end.
I was able to make the final shape this way:
1. Make the full ellipse.
2. Duplicate the layer.
3. Select the duplicate and free transform the ellipse to see the crescent of the original, at both ends.
4. Selection tool select the right half of the duplicate (I locked the original layer).
5. Free transform tool stretch the right half to reach the right edge of the original. I held Option down to make it just expand to the right.
The original issue is something to do with Flash not coping with very thin areas. As I said, I didn't get as bad a problem as you, in my case some of the bottom curve of the ellipse became straight lines.