VAA is the analog power plane, and is the output of the voltage regulator labeled MCP1 on the schematics. VAA is always at 3.3V, and VAA and VREF are tied together (accidentally), so VREF should always be at 3.3V.
Disconnecting VREF from VAA is going to be tricky, because it connects to the analog power plane in a way that's not really fixable just by cutting a trace. Well, like, you could cut the trace from VAA to the VREF pin on the chip, but then you would also be severing VREF's connection to the header, so you'd have to supply your reference voltage from a skywire or something, which would probably be unusably noisy.
Does that make sense? I feel like I'm having a hard time articulating this properly.