How can I update Apprentice?

I installed Apprentice a while ago and am updated to the Shards of Alara set. However, I cannot seem to get Conflux, M10 etc.

1) I've downloaded the patches and replaced the files, but nothing changed.

2) I then went and deleted everything except the Graphics fold and I could STILL play just as well as before. I even specifically deleted the Decks folder and I can still use all my decks.

3) When I deleted the Apprentice folder from Program Files and reinstalled, it was still able to load my decks (which were still in my recycle bin).

I just can't seem to win. The only conclusion I've been able to come to is that it is saving to some other folder (even though its Properties and save as options tell me it's going to Program Files). Is there anyone who knows a reliable way to fix this?