Weird error / Windows security profiles replaced???

[LoopTurn_]

So this isn't me, but it was my father. I am not really too experienced with how many storage devices work. So here is the run down of what happened.

 

He tried to do a backup of his computer using a disk. It didn't work but he never removed the disk. Eventually one day came and it said it started replacing security profiles. I don't even know what this means and I am better with technology then him and I am more of a programmer. A lot of programs stopped working, at the time all of the security profiles were replaced.

 

How would I go about fixing this? Is it really fixable without using a backup. I ask here because the cause was most likely that disk.

I assume it screwed up the registry but I am not 100% sure.