I had this same issue. It was strange because micropython was already on the device so I could connect with putty and interact with micropython, proof that both the RX/TX lines were working.
I then held down the boot button while plugin, and was able to reflash the device. I think that somehow my code was preventing it from working correctly as after the first time of reflashing, I no longer had to hold down the button to reflash.
Maybe same issue for you, IDK