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There are 3 separate ways to back stuff up, 2 that are stored on their servers, one that is local. They are called:
Character Settings
Client Settings
User Interface
Exactly what does each contain? Does he locally saved file contain everything that you can upload to the server? Or is Character=UI? Does it save such things as bag arrangements for for you, yer saddlebags, and all retainers?
Everything is exactly what it says it is.
Retainers and inventory have nothing to do with those.
The backups done by the launcher are local file backups saved locally. The backups done at character selection are local file backups saved to the cloud server. The button above the list of characters should backup cross-character settings (such as graphics, sound, resolution, account macros) and the button next to each character should backup the character configuration, HUD, keybinds, macros, for that specific character.
Inventory and retainer order is not stored locally in the first place. That information is already on the server.