Hi
I am a gold forum member, but have been out of the loop for awhile.
Hope you can help with this.

I will be updating some of my older WordPress installations with the latest WordPress and Atahualpa , For example I have an installation of WP 2.9.2 and Atahualpa 3.4.6.

I know that I can update my WP site and custom WP settings should be maintained, but how do I do that with Atahualpa and still maintain my custom settings?

I don’t see a way to migrate Atahualpa settings from an older version to a newer on (except for a ‘settings’ export from a newer Atahualpa version that 3.4.6)

There are two areas,
1. the basic settings which can be exported in newer versions of Atahualpa, but not in 3.4.6.
2. The custom changes I've made to the PHP files, like advertising code and other changes like changing headers or footers.

Is there a way to go from an older version to a newer version and bring over the older settings and PHP customizations?

Do I have to copy every single setting manually from the old settings and all the custom PHP files and manually copy the changes back into the new Atahualpa installation in both the settings area and the PHP files are?

Any help would be greatly appreciated.

read HOWTO: upgrade Atahualpa to a new version

For upgrading purposes, I've made a little script that will copy my files back to the newly updated theme folder.
It's quick and dirty, but it works in my case really well!
I hope you (or anybody else) can use it.

Copy the extracted file into your WP root directory and edit it to suit your needs. Run it.

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NOTE from Juggledad: You will have to edit this file to get it to work - if you do not know PHP don't bother to play with this.
1) your root folder has to be 'WP' (or you have to change this in the code)
2) your images have to be in a folder in the themes folder called 'atahualpa_images' (or you have to change this in the code)
3) you will have to remove the second array of files and the code that copies them or live with the error

This will not be supported by the moderators, so use at your own risk and if you have questions or problems, send a PM to 'Gilu' about it.
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EDIT:
Well, your comment got me thinking...
I've updated the script. All you need now is a folder in the themes directory called 'atahualpa_images' with the same structure as the original 'atahualpa' directory. The 'atahualpa_images' folder contains only the changed and new files!

The script will then copy all files from 'atahualpa_images' to 'atahualpa' and overwrite existing files!
Prior to that, it will clear the '/images/header/' directory!

Edit the script: Change

$wp_root = "./"; // if your WordPress is not in your root!
$atahualpa_images = 'atahualpa_images'; // only if you don't use this directory

That should be it!
If you have any questions, please PM me.

Something to be aware of, to quote the documentation:

Since 3.6.5 custom PHP code isn't possible anymore in the Atahualpa Theme Options.