http://www.atrixforums.com/forum/motorola-atrix-hacks/4414-how-root-motorola-atrix-all-versions-including-stock-locked-2-3-4-2-3-6-a.html
The above will get your root back for 2.3.6.
If you have an unlocked boot loader, you may want to read...
You may want to read this :
http://forum.xda-developers.com/showthread.php?t=1490283
I read another post where a developer bricked his device installing the new OTA update, w/ an unlocked BL but he was able to fix it.
Good luck.