The factor knobs have a feature called "knob lock" in the system mode, similar to catchup, except the knobs control is locked out. In this mode the the knobs still transmit midi cc's, so you could load presets on the Factors/Eclipse in tandem (via footswitches) and use the knobs to control Eclipse parameters. I know it doesn't completely solve your problem (there is no footswitch lock), but it gets you some of the way the there.
