The development of my game is coming to an end and I'm now looking into getting a hold of a publisher and publishing my game to Steam. To do this I'm also preparing my game for the use of the Steamworks SDK that handles general Steam business like achievements among other things.
The thing is my game already has a built-in achievement system and I'm worried that my achievement system and the Steam achievement system might get de-synchronized for one reason or another - as in the achievement is unlocked locally in the built-in system but not unlocked in the Steam API. This seems to have happened to several users (Plants vs Zombies example) and Steam has made it clear that this is the developer's responsibility.
How should I be a responsible developer and prevent de-synchronization or deal with it if it occurs?