Category, Main Index & Page Template is Suddenly Missing

The Category, main Index, Page Template and Frontpage PHP is Suddenly Missing from wordpress. I see the Main Index but when I click, it says no such file exists. All of the others are not even on the list anymore.

This happened soon after making the following changes:

I recently moved some gfx elements around from the right to left columns of my site. Once the code was adjusted, I copied and pasted the same code to the following:
Main Index Template / Page Template / Category Template & Frontpage PHP.

The main page still displays properly, but is missing some features like voting and comment sections for each post. Is this because I replaced code on the Front page PHP?

Why do you think this happened and more importantly how do I recreate what’s missing (if that’s the solution)? If so how? I am trying to fix this by deadline of Monday Jan 7th 2008 – your help is appreciated.

Thank you.
Contemptster.com