Hello.
I used the tip from Juggledad when updating from 3.4.9 to 3.5.1 (see below). And then I did the same to 3.5.3

So I have a lot of folders with old atahualpa-versions in them now

My question is: Which of the old ones do I dare to delete without getting problems? Can I delete 3.5.1 or do I need that?

(Update: what I actually just did was I installed 3.5.3 on my server and then activated that version instead of the old, and all settings from the old in some magical way was merged in to the new version)

All the setting are in the database so the new version will pick them up but before deleting previous versions make sure you have copied any THEME images to the corresponding folders for 3.5.3. Items such as background images or a favicon or header images.

You also need to change and paths such as background paths that had, for example atahualpa351 in it to atahualpa353.

Once you are certain all the images have been moved and paths have been changed you can safely delete the old versions. I download any images that I have uploaded to a folder on my PC for a backup and to make the next upgrade easier. You just have to remember to keep that folder updated if you add any theme related images.