Hey again,
I'm using the version control system that sets the read-only flags for files that were not checked out. So the annoying thing is when i forget to check out atlas files, they are marked read-only, unity does not overwrite some files, and the UI elements in the current scene get screwed. Only way to get them back to normal is to quit unity without saving.
Can you please add the code that checks read-only flag on files that belong to atlas before actually updating it?