The deck list has to be a clear unambiguous description of a legal deck being used by a specific player.
The cards in the actual deck have to match the deck list in such a way that the person checking the deck can quickly and efficiently establish the correspondence between the physical cards and the list.
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It is wrong IMHO for a player to write out their deck list in such a way that it requires the list-checker to refer to the reprint document when an alternative way of filling out the deck list would not require that additional work.
So in the case of the Lucarios I'd be okay with all of them listed as DP 06 as long as at least one copy of a DP 06 Lucario was present.
However if you were to play 4 Machamp HL #09, I would not be happy if you listed them as PK #11. Even though we play it as the PK reprint it is neither the same card (text change) nor can I check it by comparing the picture / name / text with a current card that is in your deck.
If you play 1PK & 3HL Machamp I would expect them to be listed on separate lines, because the deck with the HL Machamp needs an external reference outside the deck which the 4PK Machamp deck does not.
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The bottom line is that you can't go wrong if you fill the decklist in by following the instructions on the sheet! If you want to vary from those instructions in how you complete the decklist then it is your responsibility to make sure that your list isn't more difficult to check than one that had actually followed the written instructions.
That isn't a hardline position surely