I need to restart Arduino IDE after each compilations I'm using the Arduino Due and testing an I2C Scanner, the I2C Scanner works correctly but each time I want to upload a newer version of the code I get this error message :

No device found on COM11
Send auto-baud
Set binary mode


What I need to do in this case is : remove USB, restart the Arduino IDE, reconnect USB, then it works again, one time... 

It seems related to this problem : Serial port on mac only works after restarting arduino IDE

I'm not sure but What's maybe also symptomatic is I need to systematically push the restart Button of my board in order to receive something in the Serial Monitor, could it be related ? 

Here is the I2C Scanner code I'm using : 

// --------------------------------------
// i2c_scanner
//
// Version 1
//    This program (or code that looks like it)
//    can be found in many places.
//    For example on the Arduino.cc forum.
//    The original author is not know.
// Version 2, Juni 2012, Using Arduino 1.0.1
//     Adapted to be as simple as possible by Arduino.cc user Krodal
// Version 3, Feb 26  2013
//    V3 by louarnold
// Version 4, March 3, 2013, Using Arduino 1.0.3
//    by Arduino.cc user Krodal.
//    Changes by louarnold removed.
//    Scanning addresses changed from 0...127 to 1...119,
//    according to the i2c scanner by Nick Gammon
//    http://www.gammon.com.au/forum/?id=10896
// Version 5, March 28, 2013
//    As version 4, but address scans now to 127.
//    A sensor seems to use address 120.
// Version 6, November 27, 2015.
//    Added waiting for the Leonardo serial communication.
//
//
// This sketch tests the standard 7-bit addresses
// Devices with higher bit address might not be seen properly.
//

#include &lt;Wire.h&gt;


void setup()
{
  Wire.begin();

  Serial.begin(9600);
  while (!Serial);             // Leonardo: wait for serial monitor
  Serial.println("\nI2C Scanner");
}


void loop()
{
  byte error, address;
  int nDevices;

  Serial.println("Scanning...");

  nDevices = 0;
  for(address = 1; address &lt; 127; address++ )
  {
    // The i2c_scanner uses the return value of
    // the Write.endTransmisstion to see if
    // a device did acknowledge to the address.
    Wire.beginTransmission(address);
    error = Wire.endTransmission();

    if (error == 0)
    {
      Serial.print("I2C device found at address 0x");
      if (address&lt;16)
        Serial.print("0");
      Serial.print(address,HEX);
      Serial.println("  !");

      nDevices++;
    }
    else if (error==4)
    {
      Serial.print("Unknown error at address 0x");
      if (address&lt;16)
        Serial.print("0");
      Serial.println(address,HEX);
    }    
  }
  if (nDevices == 0)
    Serial.println("No I2C devices found\n");
  else
    Serial.println("done\n");

  delay(1000);           // wait 5 seconds for next scan
}
I finally solved the problem, but it's really specific and I don't know if should be on Stack Exchange. Maybe it could give some clues if someone has a similar problem one day... 

I was using pin 20 and 21 on my Arduino Due which are supposed to have built-in pull-up resistor. That's what I've read everywhere and it has been said again recently in the answer of an another question I've asked : How to chooce SDA/SCL pair on Arduino Due ?.

Solution : Since I'm using SDA1 / SCL1 with Wire1 everything works like a charm. The value I get from the device are correct, no need anymore to restart the board and I can recompile again and again without any problems. 

Edit : In fact, it work significantly better but I still had to use pullup resistors with these inputs. The goal was to use the MPU 9250 and it seems more stable now.