Someone else may have a better solution, but for a quick fix you can make a new character style in your document and name it Superscript.
Edit the character style and go to “Basic Character Formats” and leave everything blank except the POSITION field – change that to Superscript.
Click OK
Now you have a character style that will superscript stuff.
Now do a find change:
Put your registration mark in the find field: ®
and then at the bottom under the Change Format box, change it your character style.
It should find all your registration marks and change them to Superscript.
If there are paragraph styles associated with those paragraphs already, you can edit the paragraph style and go down to the GREP Style section:
Click NEW GREP STYLE
Where it says APPLY STYLE NONE – change it to your superscript character style
in the TO TEXT FIELD: Type in your ® symbol.
Click OK
Now anytime your have a registration mark in that paragraph style it will automatically be superscript.
Those are the two solutions I can think of right off the bat.
Hope that helps.
SIGH – Dwayne beat me to it.