Any setting made in the Atahualpa options are stored in the database so you will not lose any of those. This of course includes CSS settings. If you made some changes to the code itself you would have to tweak that though. That's why I typically stay away from anything outside of the options pages. You will need to copy images you added to the atahualpa folder to the new one.
Too keep the upgrade as seamless as possible what I would do is...
- Backup - Database and files
- Upload the new Atahualpa theme files into a folder called atahualpa346 (don't activate yet)
- Copy all the images you have uploaded into the various Atahualpa image folders into the new Atahualpa 3.4.6 folders. This includes favicons, header images, etc
- Use a maintenance mode plugin during low use hours and activate the new version to see how it looks
- Tweak any paths where atahualpa346 needs to replace atahualpa
- Go live when satisfied
I hope that helps