Error"Can only compare identically-labeled Series objects" and sort_index

I think you need reset_index for same index values and then comapare - for create new column is better use mask or numpy.where:

Also instead + use | because working with booleans.

df1 = df1.reset_index(drop=True)
df2 = df2.reset_index(drop=True)
df1['v_100'] = df1['choice'].mask(df1['choice'] != df2['choice'],
                                  (df1['choice'] + df2['choice']) * 0.5)


df1['v_100'] = np.where(df1['choice'] != df2['choice'],
                       (df1['choice'] | df2['choice']) * 0.5,
                        df1['choice'])

Samples:

print (df1)
   v_100  choice
5      7    True
6      0    True
7      7   False
8      2    True

print (df2)
   v_100  choice
4      1   False
5      2    True
6     74    True
7      6    True

---

df1 = df1.reset_index(drop=True)
df2 = df2.reset_index(drop=True)
print (df1)
   v_100  choice
0      7    True
1      0    True
2      7   False
3      2    True

print (df2)
   v_100  choice
0      1   False
1      2    True
2     74    True
3      6    True

df1['v_100'] = df1['choice'].mask(df1['choice'] != df2['choice'],
                                  (df1['choice'] | df2['choice']) * 0.5)

print (df1)
   v_100  choice
0    0.5    True
1    1.0    True
2    0.5   False
3    1.0    True

The error happens because you compare two pandas.Series objects with different indices. A simple solution could be to compare just the values in the series. Try it:

if df1['choice'].values != df2['choice'].values