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'Voyager' actors Ethan Phillips, Tim Russ, Garrett Wang, Robert Duncan McNeill, guest star Tom Wright, and writer Lisa Klink talked "Tuvix" at Trek Talks 3.
Best solution:
1: Sedate Tuvix. He must not be conscious for the next steps.
2: Make a transporter clone of him (like Riker/Boimler)
3: Separate one of the Tuvixes into Tuvok/Neelix, leave the other as Tuvix
Everyone wins!
Why sedate him? He willingly walked onto his execution pad.