I rooted my brothers bionic running .5.5.893 a few months ago when he just got the phone. Now we wanted to unroot to do an update then root again. I unrootrd it then we realized that he needed to back it up or he would lose his app data. So now attempting to reroot it errors in the middle of it. Is he screwed? He doesn't want t lose his data if at all possible, can we save the app data manually?
You can just take the update and reroot with motofail. All your info should be fine. There is instructions on motofail in the sticky thread "all things root guide".
Problem is that when we try to apply the update it fails, I believe because we had removed some of the factory apps that came preinstalled.
You might be out of luck. Were you using titanium backup? It sometimes makes a backup automatically. Check our SD-card or ext sd-card for a titanium backup. If it is there make sure it is on the eternal SD card and flash the 5.9.902 fxz file root with motofail and restore apps with data. Do not restore the system data as it is based on 5.5.893.