LT 3.0 online gaming question about update

I have recently flashed my xbox to LT 3.0 (my friend did the job) and I tried to sign in / bring my xbox on-line and got the following message:

A System update is available from Xbox LIVE. if you decline, you wont be able to connect to Xbox LIVE
until you take the update. Visit New Xbox Update | How to Get an Xbox 360 Update - Xbox.com for more info.

is it safe to apply that update or will i loose the flash?

Thanks!

Source: http://www.ixtreme.net/open-forum/35113-lt-3-0-online-gaming-question-about-update.html

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