[myrroddin]

I solved it, yet even though I solved the issues, I can't explain why this was necessary or what my prior method was doing wrong.

-- Process subzones
if db.watchSubZones then
    -- Battlegrounds and warfronts are the only instances with subzones
    if inInstance and instanceType ~= "pvp" then return end
 
    -- Don't loop through subzones if the player is watching a bodyguard rep
    if isWoDZone and bodyguardRepID then
        watchedFactionID = bodyguardRepID
    else
        -- Get our subzone data
        watchedFactionID = CitySubZonesAndFactions[subZone] or subZonesAndFactions[subZone]
    end
end
 
-- Get world zone data or the character's default watched faction. For some unknown reason, watchedFactionID loses data from bodyguards and instances at this stage in the code, refresh
if watchedFactionID == nil then
    if isWoDZone and bodyguardRepID then
        watchedFactionID = bodyguardRepID
    elseif inInstance and hasDungeonTabard then
        watchedFactionID = tabardID
    elseif inInstance then
        watchedFactionID = instancesAndFactions[whichInstanceID] or db.defaultRepID
    else
        watchedFactionID = zonesAndFactions[uiMapID] or db.defaultRepID
    end
end