I know what happens now.
Suppose you have Smith-14, and his father is Smith-27, and his father is Smith-39.
And you try to merge 14 and 27. This may or may not be a good idea. But anyway.
The merge completion page comes up with 14 as destination, and a choice of fathers - 39 green, 27 yellow, with yellow as default.
That is, the default choice of father to keep is the profile you're trying to merge away.
If you're awake and you tick the green box, all is well. But if you accept the default, the poor computer will try to follow your weird instructions, with weird results.