Using the latest version of the SAMD core, doing a Serial.flush() will hang forever.

Problem can be reproduced using this sketch:

void setup() {
  SerialUSB.begin(115200);
  delay(2000);
  SerialUSB.println("Start");

  Serial.begin(9600);
  Serial.flush();

  SerialUSB.println("Setup end");
}

void loop() {
  SerialUSB.println("Loop");
  delay(1000);
}

Which will only print:

15:19:30.572 -> Start

Tracing the issue down takes me to Serial.flush(), which is defined in Uart.cpp. This calls sercom->flushUART(); in SERCOM.cpp.

The previous versions of this core had the following code:

void SERCOM::flushUART()
{
  // Skip checking transmission completion if data register is empty
  if(isDataRegisterEmptyUART())
    return;

  // Wait for transmission to complete
  while(!sercom->USART.INTFLAG.bit.TXC);
}

The current version has the if(isDataRegisterEmptyUART()) commented out:

I don't understand why this is commented out, as clearly the while(!sercom->USART.INTFLAG.bit.TXC); will never return if flush() is called when the TX buffer is already empty.