IIU C, вы можете merge
на df1
со значениями, равными Y, а затем найти nans:
result = df2.merge(df1[df1["Flag_Value"].eq("Y")],how="left",on="ORDER_NUM")
print (result[result["Flag_Value"].isnull()])
ORDER_NUM REGION DRIVER Flag_Value
3 12478965 NORTH David NaN
4 25845673 SOUTH Mani NaN
5 36789156 SOUTH Tim NaN
Или даже проще, если ваши ORDER_NUM
уникальны:
print (df2.loc[~df2["ORDER_NUM"].isin(df1.loc[df1["Flag_Value"].eq("Y"),"ORDER_NUM"])])
ORDER_NUM REGION DRIVER
3 12478965 NORTH David
4 25845673 SOUTH Mani
5 36789156 SOUTH Tim