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No, I just forgot that he's a logistics expert. However, I don't see a reason why Pyre shouldn't have his machine taken away if it was taken away from Jeremy in any way.
As Vic already mentioned, everyone should have their units taken away. Because the machine represents an entire stack of level 2 units, and level 4 and higher heroes in the tavern should arrive with a single unit, not a stack. If we're being very formal about the issue, Jeremy should arrive with 1 bandit, Pyre with 1 ogre, Gurnisson with 1 wolf, etc.