The Sketch:

/* Hovermotor_Hall_Encoders.ino  Arduining DIC 10,2019
 * 
 * Code repeats every six values:
 * Hall Sensor U  0  0  0  1  1  1  0  0  0 ...  (Green cable)
 * Hall Sensor Y  1  1  0  0  0  1  1  1  0 ...  (Yellow cable)
 * Hall Sensor W  0  1  1  1  0  0  0  1  1 ...  (Blue cable)
 *                2  6  4  5  1  3  2  6  4 ...
 *                
 * Using RC Low Pass filters and a 74LS07 inverter buffer. R=1.5k and C= 0.1uF (fo=1.06kHz)             
 * -----------------------------------------------------------------------------
 * Using RobotDyn STM32F1103C8T6, STM32 ARM Arduino Mini System
 * Development board with Arduino bootloader.
 *                       STM32F1 Boards (STM32duino.com)
 *        Board:         "Generic STM32F103C series"
 *        Variant:       "STM32F103C8 (20k RAM, 64k Flash)"
 *        Upload method: "STM32duino booloader"
 *        Port:          "COM124 (Maple Mini)"
 * -----------------------------------------------------------------------------
*/
#include "LedControl.h"  // LedControl Library must be included (Use Sketch>Include Library>Manage Libraries...)

#define CLKPIN    PA2    // The CLK pin
#define CSPIN     PA1    // The CS pin
#define DINPIN    PA0    // The DIN pin
#define MAXS        1    // Using 1 MAX7219 only

#define CLEAR     PA7    // Clear the pulseCounter

#define HS_U      PB6    // STM32 Blue Pill 5 Volts tolereant
#define HS_V      PB7    // STM32 Blue Pill 5 Volts tolereant
#define HS_W      PB8    // STM32 Blue Pill 5 Volts tolereant

#define CW          1    // Assign a value to represent clock wise rotation
#define CCW        -1    // Assign a value to represent counter-clock wise rotation

#define SAMPLE_PERIOD 500  // in microseconds; should give an interrupt every 500 microseconds

char numbuff [10];

//HardwareTimer timer2(2);

LedControl Max7219 = LedControl(DINPIN, CLKPIN, CSPIN, MAXS);


void handler_Check_H_Sensors(void);

/***************************** Variables *************************************/
bool hallchanged= false;
bool checkSensors= false;

volatile byte lastcode;               // last code from the hall encoder
//volatile uint8_t lastcode;            // same as byte.
volatile byte newcode;                // new code from the encoder
volatile int change;				          // Integer variable to add or substrat to the pulseCounter
volatile int pulseCounter;				    // Integer variable to store the pulse count

byte lastInc[] = {0, 5, 3, 1, 6, 4, 2};   // Increment counter, the index is the newcode
byte lastDec[] = {0, 3, 6, 2, 5, 1, 4};   // Decrement counter, the index is the newcode

/*==============================================================================
 * setup()
==============================================================================*/
void setup()
{
  pinMode(CLEAR, INPUT_PULLUP);   // Pin CLEAR as input.
// Pins HS_U, HS_V and HS_W as inputs.
  pinMode(HS_U, INPUT_PULLUP);			
  pinMode(HS_V, INPUT_PULLUP);			
  pinMode(HS_W, INPUT_PULLUP);

  // Configuree MAX7219 8 7-segment display:
  Max7219.shutdown(0,false);  // turn off power saving, enables display
  Max7219.setIntensity(0,2);  // sets brightness (0~15 possible values)
  Max7219.clearDisplay(0);    // clear screen


// Configure channel 1 of Timer 2 to generate an interrupt every 250 microseconds.
  Timer2.setChannel2Mode(TIMER_OUTPUT_COMPARE);
  Timer2.setPeriod(SAMPLE_PERIOD);             // configures prescaler and overflow to generate a timer reload in microseconds, 
  Timer2.setCompare(TIMER_CH1, 1);

// Pins HS_U, HS_V and HS_W as interrupts . Call functions on change
  attachInterrupt(digitalPinToInterrupt(HS_U), HallSensorU, CHANGE);    // Green cable  
  attachInterrupt(digitalPinToInterrupt(HS_V), HallSensorV, CHANGE);    // Yellow cable
  attachInterrupt(digitalPinToInterrupt(HS_W), HallSensorW, CHANGE);    // BLue cable
  
  Serial.begin(115200);
  
  lastcode= digitalRead(HS_U) | digitalRead(HS_V)<<1 | digitalRead(HS_W)<<2 ;
}

/*==============================================================================
 * loop()
==============================================================================*/
void loop()
{
  Serial.println(pulseCounter);             // Display the pulse count
  sprintf (numbuff, "%08i", pulseCounter);
   for( int i=0 ; i<8 ; i++)
  {
    Max7219.setChar(0, 7-i, numbuff[i], false);
  }
  delay(100);                               // to limit the printing flow...
  if(!digitalRead(CLEAR))pulseCounter= 0;   // Reset the pulse counter.
}

/************************ Interrupt Functions *********************************/

/*-----------------------------------------------------------------------------
 * Check_H_Sensors()
-----------------------------------------------------------------------------*/
void Check_H_Sensors()   // Executed every 500 microseconds
{ 
  if(checkSensors)
  {
    newcode= digitalRead(HS_U) | digitalRead(HS_V)<<1 | digitalRead(HS_W)<<2 ;
    if (lastcode == lastInc[newcode]){
      pulseCounter--;
      lastcode= newcode;
    }
    if (lastcode == lastDec[newcode]){
      pulseCounter++;
      lastcode= newcode;
    }
    hallchanged== false;
    checkSensors= false;
  }
  if(hallchanged== true)checkSensors= true;
}

/*------------------------------------------------------------------------------
 * HallSensorW()
------------------------------------------------------------------------------*/
void HallSensorW()
{
//  hallchanged= true;
  delayMicroseconds(80);
  newcode= digitalRead(HS_U) | digitalRead(HS_V)<<1 | digitalRead(HS_W)<<2 ;
  if (lastcode == lastInc[newcode]){
    pulseCounter--;
    lastcode= newcode;
  }
  if (lastcode == lastDec[newcode]){
    pulseCounter++;
    lastcode= newcode;
  }
}

/*-----------------------------------------------------------------------------
 * HallSensorV()
-----------------------------------------------------------------------------*/
void HallSensorV()
{
//  hallchanged= true;
  delayMicroseconds(80);
  newcode= digitalRead(HS_U) | digitalRead(HS_V)<<1 | digitalRead(HS_W)<<2 ;
  if (lastcode == lastInc[newcode]){
    pulseCounter--;
    lastcode= newcode;
  }
  if (lastcode == lastDec[newcode]){
    pulseCounter++;
    lastcode= newcode;
  }
}

/*-----------------------------------------------------------------------------
 * HallSensorU()
-----------------------------------------------------------------------------*/
void HallSensorU()
{
//  hallchanged= true;
  delayMicroseconds(80);
  newcode= digitalRead(HS_U) | digitalRead(HS_V)<<1 | digitalRead(HS_W)<<2 ;
  if (lastcode == lastInc[newcode]){
    pulseCounter--;
    lastcode= newcode;
  }
  if (lastcode == lastDec[newcode]){
    pulseCounter++;
    lastcode= newcode;
  }
}