[SharinganHeir]

I couldn't actually find anything in the Tournament Guidelines about only allowing one deck, but this comes from the Penalty Guidelines:

C. Deck (List) Errors

1. Illegal Deck List
a) This type of error occurs when a player has submitted an illegal
deck list. The deck list can be illegal for multiple reasons such as an
illegal number of cards, an illegal number of duplicates of a card,
incorrect information about the players, illegible deck list, banned or
restricted cards in the deck list.
(1) Solution:
(a) The player should be found and a deck check should be
performed. Once the discrepancies have been confirmed, the
deck list should be fixed to be correct and match the deck. If the
deck is legal then the deck list should be altered to match the
contents of the deck. If the deck is also illegal, the deck should
first be fixed to be legal and then the deck list should be fixed.
This will all count as 1 penalty under illegal deck list. If the side
deck does not have the required amount of cards in it, it is
illegal and cannot be used for the duration of the tournament.
(2) Penalty:
(a) (Basic) – Game Loss (If the error is self-caught before
the start of a game, the penalty can be downgraded to a
warning.)
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(b) (Intermediate) – Game Loss (If the error is self-caught
before the start of the first round, the penalty can be
downgraded to a warning.)
(c) (Advanced) – Game Loss

2. Illegal Deck
a) This type of error occurs when a player has submitted a legal
deck lists but the deck, side deck, or reinforcement deck is illegal. This
happens if the deck doesn’t match the deck list. If the deck list is also
illegal then apply the Illegal Deck List Penalty.
(1) Solution:
(a) The player should be found and a deck check should be
performed. Once the discrepancies have been confirmed, the
deck should be fixed to match the deck list.
(2) Penalty:
(a) (Basic) – Game Loss (If the error is self-caught before
the start of a game, the penalty can be downgraded to a
warning.)
(b) (Intermediate) – Game Loss (If the error is self-caught
before the start of the first round, the penalty can be
downgraded to a warning.)
(c) (Advanced) – Game Loss

Since ALL decklists are submitted before you are entered into the tournament, it isn't possible to submit a different deck list later. If your deck doesn't match your deck list at any time during the tournament, you will be penalized for it.

Most Ninja Academy and Genin tournaments don't use decklists, but the policies don't change. If someone is known to be changing/editing their deck during a tournament, it's automatically a game loss and the deck must be corrected. It only gets worse from there.