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"Are we assuming a Pokemon (say, Vulpix) will have all its possible wild held items during a match, and be able to use all of them?"
Yes
"I was revising its equipment a few years ago, and I realized that Berry and Burnt Berry have been retconned into the Oran and Aspear berries, respectively. Should I put them down, or the original items from R/B/Y and G/S/C?"
If an item's been deleted from the game, it shouldn't be included on the profiles in general. Put down the oran/aspear berries.
Yes
"I was revising its equipment a few years ago, and I realized that Berry and Burnt Berry have been retconned into the Oran and Aspear berries, respectively. Should I put them down, or the original items from R/B/Y and G/S/C?"
If an item's been deleted from the game, it shouldn't be included on the profiles in general. Put down the oran/aspear berries.