I think the character-side LUA file contains a bit more than taxi info. For example, each character has a few settings that are character-specific, such as window locations and what items are currently being "Show..."n on the Carbonite map. I find it hard to believe these are saved outside of the SavedVariables for the specific character in question. Do note this is only my speculations, but I think the arguments are sound.
Second, Carbonite updates your taxi info every time you visit a flight master on one of the continents (as in, if you visit the Stormwind flight master, it registers all the flight masters you've visited in Eastern Kingdoms). So any loss of taxi information is easily restored by visiting any flight master in Eastern Kingdoms, Kalimdor, Outland and Northrend respectively.