Which supply items do you get to keep?

During the tutorial stages of the games, they told me that any items I take out of the blue chest will be returned at the end of the mission.

I've noticed, however, that sometimes I keep certain items that I grabbed out of the blue chest after the mission is over. For example, I have a lot of cool drinks because I rarely visit those sections of the Sandy Plains.

Which items from the blue chest do I get to keep after the mission is over?