The c-site, as with all throwing, is still in your "inventory" after you threw it. You are still holding the empty "ammo bag" of the c-site. Like, when you throw all your javelins, you still have the empty javelin bag on your back. Unless you manage to pick up something new, you will then still get the chance to have to repair it every tick. Not sure how to word it, but hope this made sense.
That being said: I STRONGLY suggest they reduce the price of the c-site. Seriously, 2.6k gold for one? That's just EVIL! I would love to see more people make equipment chest/healing tent/forward base in the game, but the HORRIBLE upkeep of the c-site just make most people not want to do it.