You need to extract the Part 2 on a new folder, update 17 isn't to be extracted OVER the Part 1.
To be clear:
1- Download the Part 1 and extract it to it's own folder.
2- Download the Part 2 and extract it to it's own folder.
If you played Part 1 until the end of update 16 and made a save at the "Save Now" screen, when you start Part 2, choose Load and your saves from Part 1 will show up, choose the one from the end of Part 1 and play. If you didn't play Part 1 to the end, I would suggest you do it. If you want to make changes to your choices from Part 1, you can instead of Load on Part 2, choose Start, and answer a bunch of questions to restart your game.
Good luck and if you need any more help, just ask.
Peace