This can happen when the connection is still open while your device resets. Windows will not close that connection but assign a new port to a device that requests a still active port.
Can you remind me of that particular batch file?
If you have multiple devices connected simultaniously (each with its own COM port), you could go with DFU flashing instead of serial.
If you just add a mode COMx 14400 (COMx is the port for the device to flash), that will switch only that one device into DFU Mode and a subsequent particle flash --usb firmware.bin will only flash that one device that is in DFU Mode (blinking yellow).