I'm not a fan of pokemon games, and I played only its first game, Leaf-Green and next, the hacked ROM version, Glazed. I'm really confused about how berries work in battles. When a pokemon used a berry in a battle, does it wear off and gets removed as an item? Because if so, then that means I would have to refill that pokemon's item slot over and over again right?
Yes, when a Berry is eaten, it's completely gone. They work like Potions and other consumables in that regard, and you can also manually use them in battle. So once the battle is over, they have to be replaced if you want your Pokémon to automatically use them in battle again.
Other held items are also consumed when used, like the Absorb Bulb or the Focus Sash, but they can't be used manually, their effect activates automatically when certain conditions are met.
There are also held items, like Leftovers and Quick Claw, that are never consumed, and passively provide their effect for as long as they're held.