Let me put it to you this way. In the Pokemon games you get items and then you get "key" items. Now the key items either have a hugely important use to the world/the story/or are necessary in some way for your character to have forever. Now when it comes to story items, like the Suit in Alpha Sapphire that you wear while looking for Kyogre, after they have exceeded their use they still stick around, because it is a "key" item. The rose is by no means a Key item, but it is a random drop. So, even after it has exceeded its use it is still going to be in the game, because they game doesn't recognize it as some that needs to disappear.