Вот один с np.unique
-
unq,idx,c = np.unique(a, return_index=True, return_counts=True)
unq_idx = np.sort(idx[c==1])
a_out = a[unq_idx]
b_out = b[unq_idx]
Пробный прогон -
In [34]: a
Out[34]: array([1, 2, 2, 3])
In [35]: b
Out[35]: array(['a', 'd', 'f', 'c'], dtype='|S1')
In [36]: unq,idx,c = np.unique(a, return_index=1, return_counts=1)
...: unq_idx = idx[c==1]
...: a_out = a[unq_idx]
...: b_out = b[unq_idx]
In [37]: a_out
Out[37]: array([1, 3])
In [38]: b_out
Out[38]: array(['a', 'c'], dtype='|S1')