I apologize if this is an inappropriate question; I think it is more related to wordpress then the theme but just in case anyone has advice...

I have a non-wordpress website. I just developed a new website using wordpress as a cms and atahualpa as my theme. I want to move the new website to the domain.

I have the current website under: http://domain.com/en

My new wordpress version is under: http://domain.com/new/en

I've done the switch, keeping all the old pages in the directory /en, but adding the wordpress files and swapping out the indexes. I've now switched it back to the original index, because after doing the switch, only the new index shows - nothing else. The links appear to have all changed (I made the switch after changing the general settings to the new site directory in the dashboard)... but no luck getting any pages to work except the index.

Any advice?

Did you change the paths for the WordPress site in the database? The URL paths in the WordPress general settings would be different after you moved the site so would need to be changed. You can either do that before the move or after via PHPMyAdmin. If you do it before the move you will be locked out of the WP dashboard until the files have been moved so I ofter move and go into the options table afterwords amd change the paths.

Note you can also export the SQL before changing the URL
EDIT the export and do a global change (find old url, replace with new url)
Import it to the new database.

The database changed automatically. I ended up getting it to work by changing wp-config as described here:
http://codex.wordpress.org/Changing_The_Site_URL