As Nick said, you'll effectively be changing the preset when you change an algorithm, but you're exploring an area of interest to me. I can't give a recipe, but the presets seem to load in a memory buffer area (Preset 0, with algo-specific default values?).
I picked up some pertinent documentation from this thread. TJsysex gives you the supported data types, and PresetFormatDescription fleshes out the information. It sounds to me like you'll need to provide Product Type and the encoder Algorithm Index at a minimum.
I have a few earlier Novation ReMote keyboards here. In those, you can only send 20 bytes of sysex, including the Data Value insertion point, and the F7 (EOX) message. Best of luck with this, and let me know what you come up with.
If it were me, I'd have approached this with something like Bome's SendSX, and modified some existing sysex dumps. I'd be interested in the results of a more convenient approach [using a MIDI controller], though.
