Apparently, the new Ice Cream Sandwich update for the Transformer Prime breaks root, (which really isn't much of a surprise). Luckily, we have an amazing community working hard to come up with a work-around so everyone who is already rooted can still get the update. In the mean time, if you are concerned about it, you might manually hold off on getting the OTA update for your Transformer Prime, until there is a good solution.
We will keep you updated, and/or if you see a good workaround with detailed instructions, please post in this thread to share with everyone.
Source: TransformerForums via AndroidPolice