I have two unrelated projects, A.sla and B.sla.
Images for ProjectA are located in a folder called ImageA.
Images for ProjectB are located in a folder called ImageB.
If I open and work on A.sla, then open B.sla, I would like B.sla to remember that the images it uses are in the ImageB folder, not in the ImageA folder I was using for the other project. Changing the folder where I have an image seems to change the settings globally, not for an individual sla [similar issues also with where I print a PDF etc]
these image folder, were they created manually? or did you do a collect for output for these two documents? if the former, then open the documents and do a collect for output "save". you will be prompted to create a save folder, i'm not sure if it will work with the current folders you have, but i dont think it should be an issue. the collect for output function will create a sub-folder for the images for that document. and scribus should reference the image directories separately for the respective documents.
let us know if this works for you.