MIDI Continuous Controller assignments are written to a system file and should remain in effect until changed. Note that the CC assignments for synth lines 1 and 2 are separate for each of the eight Multi Mode voices. By contrast, assignments for the so-called performance controls, e.g. Chorus, Ring Mod, Sub Osc, etc., are global and will remain in effect regardless of which Multi Mode voice is in effect.
Are you saying that CC assignments you have made are not working at all, or between sessions?