Starting in June.
The FAQ for YCS Secaucus has been updated to include an update for the End of Match Procedure. The tl;dr version is “you don’t count turns”, but since that only rises further questions, read the whole FAQ to see what to do depending on whether you are on swiss or single-elimination rounds.
Q: What happens if I am not done with my Match after 40 minutes? UPDATED!
A: Starting on June 1st, 2018, all Yu-Gi-Oh! TCG Organized Play will use brand-new End of Match procedures. Duelists should familiarize themselves with the new End of Match procedures prior to attending any event.
Sometimes a Match will not be finished when the time ends for a round. If this happens, it is both Duelists’ responsibility to note whose turn it is when time is called. Duelists who require assistance with the End of Match procedures should raise their hand and call for a judge. The judge should be notified that the Match is ongoing and whose turn it is. The judge may or may not stay to supervise the End of Match procedure, but should ensure that both Duelists understand the following procedures.
End of Match procedures should follow these three (3) rules:
Rule #1: If time is called while Duelists are in the middle of a Game, the current Game must have a decision (Win, Loss, or Draw)
Rule #2: Once the current Game has concluded with a decision, determine the winner of the Match by determining the number of Game Wins (or Game Losses) each Duelist has for the current Match. The Duelist with the most Game Wins will win the Match.
Swiss Rounds: If both Duelists have the same number of Game Wins, or if time was called in between games of a Match when both Duelists had the same number of Game Wins, then the Match is a Draw.
Single-Elimination Rounds: If both Duelists have the same number of Game Wins, or if time is called in between Games of a Match while both Duelists have the same number of Game Wins, they will begin a new Duel with specific guidelines.
Neither Duelist may use his or her Side Deck. If time was called in between Games of a Match and at least one Duelist has already accessed his or her Side Deck, then both Duelists may use their Side Deck.
Duelists must use a random method (die roll, coin flip, etc.) to determine who will go first.
The Duel will continue for a total of four (4) turns, two (2) turns for each Duelist, unless a Duelist manages to win the Duel before the four (4) turns have concluded.
A “turn” is defined as the start of the Draw Phase until the end of the End Phase for a single Duelist.
Once the four (4) turns are completed, Life Point totals are compared and the Duelist with the highest Life Point total wins the Match.
If both Duelists’ Life Points are the same after the four (4) turns are completed, then play will continue on a turn-by-turn basis, with the Duelist with the most Life Points at the end of a turn being declared the winner of that Game.
Rule #3: If a win condition occurs during End of Match Procedures, that Duelist wins the current Game.
Keeping these three (3) rules in mind, please follow these instructions when proceeding to End of Match procedures:
Continue with the current Phase of the Game. Once the Phase is over, stop the game.
Determine a Game Winner at this point, with the Duelist with the most Life Points winning the Game.
During Swiss Rounds, if both Duelists’ Life Points are the same, the Game is a Draw. Compare Game Wins with the Duelist with the most Game Wins winning the Match. If the Game Win totals are the same, the Match is a Draw.
During Single-Elimination, if both Duelists’ Life Points are the same at the end of the current Phase (Step 1 above), finish the current turn. If both Duelists’ Life Points are the same at the end of the turn, then play will continue on a turn-by-turn basis, with the Duelist with the most Life Points at the end of a turn being declared the winner of that Game.
Match Draws cannot occur during Single-Elimination Rounds.
Source: FAQ for the first YCS since June.