You could make this with a Shining Armor-colored gem...



I imagine Shining Armor's gem being a shield, with the center being Element of Magic-esque, and with the outer of the shield being alexandrite blue when not swapped due to an altering, and the center being garnet red when not swapped due to an altering... And after the "altering", it would be apple green, with an apple red center.



I imagine Doctor Whooves' gem being this hourglass, with an arctic gem blue color on the top when not swapped due to an altering, and tangerine gem orange coloring on the bottom when not swapped due to an altering... And after the "altering", it would be alexandrite blue on the top, and garnet red on the bottom.



I imagine Big McIntosh's gem being his apple cutie mark, with the outer bottom being apple green, and with the center bottom, leaf, and stem being apple red, all before the altering... After the "altering", it would be arctic gem blue, with a tangerine gem orange center bottom, leaf, and stem.