FFXI avoided continuity errors by not including characters whose status quo ever changed in sidequests. (Or, in the case of the Shantotto expansion, having exceedingly lame excuses for NPCs remaining in place when they shouldn't.) It would be a waste of effort to account for every possibility, so if you want continuity, it means that any character that appears in any non-MSQ quest can never, ever die or have their status significantly changed. I'm willing to accept story contradictions to avoid that.