How do I get rid of duplication

The reason for two arrays seems to be to keep the two PWM boards separate. How about adding a function to direct the data to the correct board? Then the two arrays can be consolidated into one:

#include <Wire.h>
#include <Adafruit_PWMServoDriver.h>
#include <CMRI.h>
#define MIN_PULSE_WIDTH       95
#define MAX_PULSE_WIDTH       530
#define FREQUENCY             50

Adafruit_PWMServoDriver pwm0 = Adafruit_PWMServoDriver(0x40);
Adafruit_PWMServoDriver pwm1 = Adafruit_PWMServoDriver(0x41);
CMRI cmri(0, 96, 32);     //CPNODE with address 0, 96 inputs, 32 outputs


struct turnoutData
{
  byte Tbit;                 //0 or 1 from external program
  int  targetPos;            //based on Tbit, set to either pos1 or pos2
  int  pos1;                 //servo position 1
  int  pos2;                 //servo position 2
  int  offset;               //horn offset from 90 degree position added to targetPos before sending to servo
  byte relayPin;
  byte relayState;           //set to either relayState1 or relayState2 based on Tbit value
  byte relayState1;          //servo's corresponding relays position 1 state
  byte relayState2;          //servo's corresponding relays position 2 state
  int  currentPos;           //used to use slow motion to move servo from position to position
};

struct turnoutData turnArray[] =
{
  // First PWM board
  { 0, 312, 249, 375, -40, 35, 0, 1, 0, 312},           //312 is 90 degrees,  249  is 70 degrees, 375 is 110 degrees
  { 0, 312, 249, 375,  20, 67, 0, 1, 0, 312},
  { 0, 312, 375, 249,  -9, 30, 1, 0, 1, 312},
  { 0, 312, 249, 375,  12, 68, 0, 0, 1, 312},
  { 0, 312, 249, 375,   0, 32, 0, 1, 0, 312},
  { 0, 312, 249, 375,  14, 33, 0, 1, 0, 312},
  { 0, 312, 312, 312,   0, 70, 0, 0, 0, 312}, //Future use
  { 0, 312, 312, 312,   0, 70, 0, 0, 0, 312}, //Future use
  { 0, 312, 312, 312,   0, 70, 0, 0, 0, 312}, //Future use
  { 0, 312, 375, 249,   2, 69, 0, 1, 0, 312},
  { 0, 312, 375, 249,   6, 64, 1, 0, 1, 312},
  { 0, 312, 375, 249,   9, 66, 1, 0, 1, 312},
  { 0, 312, 375, 249, -31, 65, 0, 1, 0, 312},
  { 0, 312, 375, 249,  18, 63, 1, 0, 1, 312},
  { 0, 312, 375, 249,  -9, 62, 0, 1, 0, 312},
  { 0, 312, 375, 249,   0, 31, 0, 1, 0, 312},
  // Second PWM board
  { 0, 312, 249, 375, -19, 23, 1, 0, 1, 312},
  { 0, 312, 249, 375,   6, 25, 0, 1, 0, 312},
  { 0, 312, 249, 375, -23, 29, 1, 0, 1, 312},
  { 0, 312, 249, 375, -16, 22, 0, 1, 0, 312},
  { 0, 312, 249, 375,  -6, 28, 0, 1, 0, 312},
  { 0, 312, 249, 375,   0, 24, 1, 0, 1, 312},
  { 0, 312, 375, 249,   0, 27, 0, 1, 0, 312},
  { 0, 312, 249, 375,  -1, 26, 1, 0, 1, 312},
  { 0, 312, 375, 249,  -9, 34, 0, 1, 0, 312},
  { 0, 312, 312, 312,   0, 70, 0, 0, 0, 312}, //Future use
  { 0, 312, 312, 312,   0, 70, 0, 0, 0, 312}, //Future use
  { 0, 312, 312, 312,   0, 70, 0, 0, 0, 312}, //Future use
  { 0, 312, 312, 312,   0, 70, 0, 0, 0, 312}, //Future use
  { 0, 312, 312, 312,   0, 70, 0, 0, 0, 312}, //Future use
  { 0, 312, 312, 312,   0, 70, 0, 0, 0, 312}, //Future use
  { 0, 312, 312, 312,   0, 70, 0, 0, 0, 312}, //Future use
};

void SetPWM(int channel)
{
  if (channel < 16)
    pwm0.setPWM(channel, 0, turnArray[channel].currentPos + turnArray[channel].offset);
  else
    pwm1.setPWM(channel - 16, 0, turnArray[channel].currentPos + turnArray[channel].offset);
}

void processTurnouts()
{
  for (int i = 0; i < 32; i++)
  {
    if (turnArray[i].Tbit == 1)
      (turnArray[i].targetPos = turnArray[i].pos1);
    else
      (turnArray[i].targetPos = turnArray[i].pos2);

    if (turnArray[i].targetPos != turnArray[i].currentPos)
    {
      if (turnArray[i].targetPos > turnArray[i].currentPos)
      {
        turnArray[i].currentPos += 2;
        if (turnArray[i].currentPos >= turnArray[i].targetPos)
        {
          turnArray[i].currentPos = turnArray[i].targetPos;
        }
        SetPWM(i);
      }
      else
      {
        turnArray[i].currentPos -= 2;
        if (turnArray[i].currentPos <= turnArray[i].targetPos)
        {
          turnArray[i].currentPos = turnArray[i].targetPos;
        }
        SetPWM(i);
      }
    }

    if (turnArray[i].currentPos == turnArray[i].pos1)
      turnArray[i].relayState = turnArray[i].relayState1;
    else
      turnArray[i].relayState = turnArray[i].relayState2;
  }
}

void setup()
{
  Serial.begin(57600);
  Serial.println("JMRI CMRI Arduino Mega Interface");
  Wire.setClock(400000);
  pwm0.begin();
  pwm0.setPWMFreq(FREQUENCY);
  pwm1.begin();
  pwm1.setPWMFreq(FREQUENCY);

  for (byte i = 0; i < 32; i++)
  {
    pinMode(turnArray[i].relayPin, OUTPUT);
    digitalWrite(turnArray[i].relayPin, turnArray[i].relayState);
  }
  Serial.println("Init completed.");
}

void loop()
{
  cmri.process();
  for (byte i = 0; i < 32; i++)
  {
    turnArray[i].Tbit = cmri.get_bit(i);  //store bit from external computer
  }
  processTurnouts();
  for (byte i = 0; i < 32; i++)
  {
    cmri.set_bit(i, turnArray[i].relayState );      //send relayStates back to computer
    digitalWrite(turnArray[i].relayPin, turnArray[i].relayState);
  }
}