So, if I'm understanding correctly, the LED won't flash when you get a new message?
(If I'm wrong and you just want to change the color of the LED, please don't read any further.)
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Does it flash at all? IE: Text messages, missed calls, voicemails, etc?
If not, then are you're sure that the notification light is on?
Got to: Settings - Display - Notificaiton Light
If the above is set, and you are receiving the light from other apps; how about the Notifications settings to the email app?
If you're using the stock email app, open it and then tap on the three dots at the top right.
Go to Settings - Select your account - scroll down to Notifications and make sure that is checked.
Even if you don't want it to make a noise, or vibrate, it still has to be checked for the light to work.
If all of the above is correct and set, then the only other option I'd have for you would be painful.