There are no easy way to remove the duplicate brushes. I suggest that you should remove the duplicated brushes from one of your brush set manually and save it as new brush set.

Or remove the duplicate brushes from both brush set. And also save the duplicated brushes as new brush set.

The bad news is you have to do it all manually. But this will save your time for the next time you load those brush set.

for example, 1 brush set .abr file contains 50 brushes and another .abr file contains 30 brushes, but when you load the 2 you realize they each contain 10 of the same brushes…