I have a friend that wants to convert to Atahualpa after using a very restrictive theme. The only catch is that the theme has a bunch of Custom Post templates.

What will happen to the existing Custom Posts if I just activate Atahualpa? Will they be preserved into default format? And if so, what happens to the Custom Field content?

Is there a clean way to preserve the Custom Post types? I'm assuming I have to make new templates. Do I just have to duplicate the Custom Fields into the new templates?

Thanks!

You could try the 'Custom Post Type UI' plugin

I don't believe this plugin has an export function. Does the standard WP export tool support Custom Post Types or is there another plugin that works for that?

To the best of my knowledge, all the data that makes up the custom posts is stored in the normal wp database tables

This plugin imports Custom Post Types from CSV:

http://wordpress.org/extend/plugins/csv-importer/

However, the native WP exporter is in XML. Is there a way to export as CSV?

did you try the plugin I mentioned? if you are worred about the database do a backup before you do anything else.