A Domain can point at specific files across one or more repositories, so an agent can be handed not just your written notes but the exact file it should double-check against them.
Turning a Domain on for a workspace automatically brings its linked repositories along with it — a Domain whose repository isn't attached can't resolve the files it points to, so this happens for you rather than becoming a step you have to remember.
Turning a Domain off again doesn't remove those repositories — they might be shared with another Domain, or you may have added them yourself for an unrelated reason. It only ever adds, never silently takes away.