Don't know if this will help with merge points in your situation, but when the points of a model won't merge I just select all the points I want to merge and do a fixed distance merge less then the minimum distance of the closest points in the selection I don't want merged, then merge and point count should be half the originally selected # of points- if more something didn't merge and get welded and if less, something merged that shouldn't have and gets undo'd and a smaller fixed merge is chosen. If that makes any sense at all..
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Meandering to a different drummer..
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