I gave my magmortar a fire gem and was using magmortar to fight in the elite four. After the fights got over I noticed that the fire gem was missing, I surely do remember not taking it out, then why did the fire gem disappear??? Does it gets consumed???
Gems,scarves,herb and berries are all one use item, therefore while fighting with the E4 the gem would have been used and thus disappeared.
Only In Online battles,subway battles these items don't get used up
All Gems can only be used once. After they have been used once, they are gone forever. However, if used in a online battle or versus a friend, it will be returned to you after the battle. You can also use the move Recycle or ability Pickup to retrieve the Gem during any battle, including ingame battles.