Without Steam, collecting achievements in the same place requires using the same /user/ data each time. So you can copy the /user/ directory to other places (or specifically /user/game.bin) when intending to play elsewhere and wanting to maintain an ongoing record of achievements, lore, collected items, learned hacks, etc. It's not possible* to merge multiple data sets after the fact.
*The exception is if you're playing via Steam and have cloud saves activated, in which case it always uploads your metadata and will download it wherever you play through Steam. Achievements in particular actually don't even require cloud saves, because it'll check your account for earned achievements that the local copy doesn't know about and download them automatically (though I'm guessing you're not using Steam).
