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I'm using version 6.x-2.2 of the Taxonomy Manager module and have found that when you try and merge terms with incorrect syntax, both terms are deleted.
1. Create a new vocabulary with terms to merge. In this example, my term ids are 6 and 7.
2. Select the two terms to merge.
3. In the Resulting merged term box, enter "taxonomy-term:". After pressing merge, both of your terms will be deleted.