Pandas check if row exist in another dataframe and append index

you can do it this way:

Data (pay attention at the index in the B DF):

In [276]: cols = ['SampleID', 'ParentID']

In [277]: A
Out[277]:
   Real_ID  SampleID  ParentID Something AnotherThing
0      NaN        10        11         a            b
1      NaN        20        21         a            b
2      NaN        40        51         a            b

In [278]: B
Out[278]:
   SampleID  ParentID
3        10        11
5        20        21

Solution:

In [279]: merged = pd.merge(A[cols], B, on=cols, how='outer', indicator=True)

In [280]: merged
Out[280]:
   SampleID  ParentID     _merge
0        10        11       both
1        20        21       both
2        40        51  left_only


In [281]: B = pd.concat([B, merged.ix[merged._merge=='left_only', cols]])

In [282]: B
Out[282]:
   SampleID  ParentID
3        10        11
5        20        21
2        40        51

In [285]: A['Real_ID'] = pd.merge(A[cols], B.reset_index(), on=cols)['index']

In [286]: A
Out[286]:
   Real_ID  SampleID  ParentID Something AnotherThing
0        3        10        11         a            b
1        5        20        21         a            b
2        2        40        51         a            b