When I get a new appearance or something checked off it is no longer properly updating or removing said item from my list. It put the blue check on the side of it item but its not refreshing even when I reload the full addon.

Try Shift + Left Clicking the header. When an item has a timer on it, Blizzard's API "loans" you the appearance. The next time you login, that status returns false until you interact with the API again. You can force this interaction by Shift + Left Clicking the header. If this issue is still a problem, please submit a new ticket.