Well, today I learned Hammer clones entities between maps when run through the compiler.
e.g. In map A, I pick up the HEV Suit, and go through the trigger_changelevel to map B. I go back through the changelevel (immediately or after waiting a bit, it doesn't matter) to map A, and another HEV Suit is there, waiting to be taken. Same thing happens with monster entities if they've moved from their original spawn point. To my knowledge, brush-based entities and things like ambient_generic, light, etc. aren't cloned; just monsters and items.
This is just the game engine keeping track of things as you move between the levels. If you kill a monster then go forward a level and come back the monster should not spring back to life, the engine keeps track.
No "cloning" occurs.