Despite all the talk, relatively few mergers have actually occurred in the nonprofit world, and most of those are really take-overs of struggling organizations, not mergers of equals. Where the acquired organization has a checkered history--and uncertain potential liabliities--it probably makes sense to delay a true merger and take control in a way which protects the assets of the acquiring entity.
This Ready Reference Page discusses the many ways that control can be passed to another organization.
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