Since you are using a Mega2560, just connect your modbus to Serial1 (Rx1=pin19, Tx2=18) instead of Serial. Serial is the only port connected to the Serial Monitor.
void setup() {
//Encoder
pinMode(21, INPUT_PULLUP); // internal pullup input pin 21
pinMode(20, INPUT_PULLUP); // internal pullup input pin 20
//Setting up interrupt A rising pulse from encodenren activated ai0(). AttachInterrupt 2 is DigitalPin nr 20.
attachInterrupt(2, ai0, RISING); //0 & 1 taken by RS485
//B rising pulse from encodenren activated ai1(). AttachInterrupt 3 is DigitalPin nr 21.
attachInterrupt(3, ai1, RISING); //0 & 1 taken by RS485
//Encoder
//RS 485
pinMode(MAX485_RE_NEG, OUTPUT);
pinMode(MAX485_DE, OUTPUT);
// Init in receive mode
digitalWrite(MAX485_RE_NEG, 0);
digitalWrite(MAX485_DE, 0);
//RS 485
Serial.begin(9600); // for debugging
Serial1.begin(9600); // for modbus
pinMode(RELAY1, OUTPUT);
digitalWrite(RELAY1, HIGH); //RELAY 1 is OFF
// Modbus slave ID 1
node.begin(1, Serial1);
...