Попробуйте:
df.drop(df.index[rm_indexes])
пример :
import pandas as pd
df = pd.DataFrame({"A":[0,1,2,3,4,5,6,7,8],
"B":[0,1,2,3,4,5,6,7,8],
"C":[0,1,2,3,4,5,6,7,8]})
pos = [0,2,4]
df.drop(df.index[pos], inplace=True)
вывод
A B C
1 1 1 1
3 3 3 3
5 5 5 5
6 6 6 6
7 7 7 7
8 8 8 8
РЕДАКТИРОВАТЬ , после дополнительной спецификации, предоставленной OP: несколько строк с одинаковым индексом
df = pd.DataFrame({"A":[0,1,2,3,4,5,6,7,8],
"B":[0,1,2,3,4,5,6,7,8],
"C":[0,1,2,3,4,5,6,7,8],},
index=["a","b","b","a","b","c","c","d","e"])
df['idx'] = df.index
pos = [1]
df.reset_index(drop=True, inplace=True)
df.drop(df.index[pos], inplace=True)
df.set_index('idx', inplace=True)
вывод
A B C
idx
a 0 0 0
b 2 2 2
a 3 3 3
b 4 4 4
c 5 5 5
c 6 6 6
d 7 7 7
e 8 8 8