Which IDE are you using? Are you using the normal 'web IDE' that you've used with serial devices before, or are you using the 'Native IDE' from http://www.espruino.com/Web+IDE#as-a-native-application ?
Unfortunately until Google adds Web Bluetooth support for Chrome on Windows you have to use the Native version.
The COM port stuff is a red herring - The Bluetooth LE UART never appears as a Windows COM port, so you won't see (or be able to connect) to it via the built-in windows COM port menus.
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