This trope usually happens a substantial amount into the game; either the player's entire inventory is removed or some portion of it. This frequently occurs due to the player being captured.
Often this is done to add challenge or to change the gameplay for the next (or final) part of the game. In most cases, players are able to find replacement items or retrieve what they lost from a container.
Some well known examples of this are in Half Life 2 where players lose their armaments, but also gain a new weapon in the process; several times in Fallout 3 and its DLC; Assassin's Creed (at the very beginning of the game); and at the end of Half Life (Players still keep their HEV suit).