They'll likely reset to a predetermined preset that is programmed into the ECU, the CO will still need to be set as it changes with air pressure, elevation, etc.. the TPS may also go back to a preset value, but that value may not be what is necessary for the bike to run correctly.
I don't know about a 999 but (and I think it's the same) on a 916 the TPS is a physical, positional setting that will not move because the battery is removed, as is the CO setting which is done either by a screw (air bypass) or trimmer in the ECU, again removing the battery will not have any effect on this as they are mechanical positions.
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