Do it in two steps.
First, temporarily underline any “Ref.+number” string with red:
1. Find What: Ref.^#
2. Replace With: ^&
+ Format=red underline

Then, search for red underlined text that is superscripted.

This will give you all superscripted numbers associated with “Ref.”.

When you have finished dealing with the superscripted numbers, remove the temporary red underline.

HTH.
Cheers,
Robert