If it's the 300MB+ update, that is the one I was telling you to install before you did anything with the phone, lol. If you ONLY installed root and have not modified any files or installed recovery, you can update. But after the update you will have to factory reset and then root again.
Samsung Galaxy S® 4 MJA Rooted with CF Auto-Root Tutorial
HTC EVO Design 4G™ v4.0.3 Bootloader Unlocked & Rooted with HTC SuperTool v3
If it ain't broke, use a sledge hammer.