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When a card says to permanently change something, it means that the modifications will persist until the end of the game, no matter what happens to the card or if it enters another zone.
Transform is a specific case of a permanent modification, where the card becomes a completely different card, instead of just being altered in some way.
Permanent modifications can be undone by using the Revert mechanic, or in some cases, but applying the opposite permanent modification (+1 and -1).