Is it impossible to S-Rank this game now?   
 
New copies of old achievements are available since the game updated.  You can't seem to get the old copies of the achievements.  For instance, I just completed China Shop, and only got credit for one copy of that achievement.  I had gotten others, like Ask Me About Mustache Mode before and after the update, so I now have two copies of that achievement. 
 
Can these copies be merged, or are we just SOL?

It updated most of my achievements through steam, the only one that didn't update was the complete all 20 mini games.  Apparently you have to start a new game in order to do it.  I'm not sure what platform you play it on, but when GOTY came out, steam updated it automatically.

Yeah, they're fine on Steam, but on Giant Bomb, there are two copies of several of the achievements.  I had already played the game through once before the GOTY version came out, so I had several of those.  When I played through after GOTY, I got those achievements again on Giant Bomb. For instance, I've been credited China Shop once, but there's another copy of that achievement that I wasn't given.
 
It doesn't really matter, but it's kind of a weird situation.  It seems that anybody who plays PvZ on Steam from here on out won't be able to S-Rank it.  Shame.

I know what you mean, I had an S-rank before the update and for some reason I remove my steam account sync and then re-added and those old achievements are no longer computed which is a shame. But only for statistics purposes since I'm about to s-rank again (only the 20 mini-games and the 2 gargantuan ones left) and it will be on my page on steam and even here if one takes some time to notice that the only achievements I'm missing are the doubled ones.

I have the same problem .