There are more issues with Atlas Builder (I have the one that came with editor patch 1.11.1).
I need to replace some images in my atlas but I need them to have a different name and when I drag and drop an image into images window it instead duplicated an existing sprite(usually the first one in the atlas).
Sometimes I want to add new sprites in between old ones and the same thing happens.
Importing an image puts it at the bottom of the list, I can drag and drop it in between sprites but that sometimes moves by mistake other sprites that I hover over which then messes up all the ids.
All this replacing existing images would be unnecessary if you could edit each sprites ID.
I'm currently stuck as what to do... I can't change the existing atlas properly and I can't go into each effect and change all of the IDs all over again because I have hundreds of them.