I performed some experiments and have some suggestions.
Attached is a project based on your original design intent. It has three schematic sheets. Enable only one sheet at a time. Disable the enabled sheet first, then enable the next sheet. Perform a build.
The application in main() switches the AMux_1 one channel every 1 second and displays the mV reading using the DEBUG_UART @ 115.2Kps.
The "sch" is a modification of your original design (See pic below). I included 3000mV and 500mV VDAC sources to drive the channels 0 and 1 of AMux_1.
The 1.024V Vref is not AutoEnabled. The resultant channel 3 voltage reading is 1824mV. There is also a Opamp follower mode on the output of the AMux_1 to see the result of the mux on a scope.
The "VDAC" sheet (See pic below) replaces the 1.024V Vref with a VDAC generating 1.020V. The resultant channel 3 reading is about 1042mV. This is more on target.
The final "VFD" sheet (See pic below) keeps the 1.024V Vref on channel 3 with it AutoEnable'd. It does replace Comp_1, Comp_2, Comp_3 and Comp_4 with a 4-channel VFD component. The resultant channel 3 voltage is about 1042mV. I did not fully configure the VFD so it may not be working to intended spec.
By the way, Cypress provides a PowerMonitor that provides ADC readings and input voltage fault detection of various types.
Maybe one of these ideas will work for you.
Len "Engineering is an Art. The Art of Compromise."