Rule R2 is quoted below for reference, with some portions bolded for emphasis.
<R2> One Robot per Team. Only one (1) Robot will be allowed to participate per Team in the VEX IQ Challenge. Though it is expected that Teams will make changes to their Robot at the event, a Team is limited to only one (1) Robot, and a given Robot may only be used by (1) Team. The VEX IQ system is intended to be a mobile robotics design platform. As such, a VEX IQ Challenge Robot, for the purposes of the VEX IQ Challenge, has the following subsystems:
Subsystem 1: Mobile robotic base including wheels, tracks, or any other mechanism that allows the Robot to navigate the majority of the flat playing Field surface. For a stationary Robot, the robotic base without wheels would be considered Subsystem 1.
Subsystem 2: Power and control system that includes a VEX IQ legal battery, a VEX IQ control system, and associated Smart Motors for the mobile robotic base.
Subsystem 3: Additional mechanisms (and associated Smart Motors) that allow manipulation of Game Objects or navigation of Field obstacles.
Given the above definitions, a minimum Robot for use in any VEX IQ Challenge event (including Robot Skills Challenges) must consist of subsystem 1 and 2 above. Thus, if you are swapping out an entire subsystem of either item 1 or 2, you have now created a second Robot and are no longer legal.
Because you are swapping all wheels for a functionally different drive system, this would be considered a complete swap of Subsystem 1, and would therefore not be legal.