After flashing the USB/serial device gets left in an odd state.
I have found if you connect with a serial programme ( screen on linux, putty ) on windows with a baud of 115200 after flashing, you get a command prompt. Then quit this, and try the connection from the web ide with baud rate 115200.
The other related factor is the ESP8266 outputs on the UART and boot at 76800 baud and spits out:
ets Jan 8 2013,rst cause:1, boot mode:(3,7)
load 0x40100000, len 25336, room 16
load 0x3ffe8000, len 2544, room 0
load 0x3ffe89f0, len 1044, room 8
I think this output confuses the web ide, an if you look in the console you see 'overrun' or something similar, and the nodejs serialport connection is disconnected. Perhaps this could be commented out and see if this works a work around?