typically,clockwork recovery will not install an OTA,unless its packaged up by a developer into a flashable .zip file. however,i have read instances of peoples phones trying to install the update,and not even notifying the owner that an update was available

one instance,the guys phone was just booting into recovery over and over. another,it caused a bootloop that required him to go back to stock.
your best bet is to pay attention to the forums so that you can always make sure youre running a rom based on the most current firmware. that way your phone wont try and update.
there have been a couple other threads on this,theres a little more info here:
http://androidforums.com/thunderbolt-all-things-root/327706-will-updating-get-rid-my-root.html