Is it ok for the soft tissue to brush up against the live rock.

If the tissue is constantly moving back and fourth across the rocks there might be some issues, but other than that you should be ok IMO.
 
I had a hammer that one side was rubbing against some rock and it started to become a whitish color, I moved it to a different location (near a Torch) and I dipped it with Lugols, but it didn't last wrong as my Torch did a number on it. So yes keep a eye out on it
 
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