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Yup, be sure to be on a stock ROM before you do it, and remember that you have to have root to restore TA. The standalone TA tool (from the cross dev section) restores and locks the bootloader, so no need to do it again in Flashtool after you've restored TA.
Worst case scenario: You restore TA and lock the bootloader and the device won't turn on, and all you get is a simple vibration and a blinking red light. Open Flashtool and unlock the bootloader again. This will happen if you're not on stock kernel (i.e you have recovery), so be sure to be on stock ROM w/ stock kernel.