As mentioned in the docs, you need to use the axis
option there, because without it being mentioned it would delete elements on a flattened version. Thus, you need to do like this -
np.delete(mytupList,indxList,axis=0).tolist()
Sample run -
In [21]: mytupList
Out[21]: [(1, 2), (2, 3), (5, 6), (8, 9)]
In [22]: indxList
Out[22]: [1, 3]
In [23]: np.delete(mytupList,indxList).tolist() # Flattens and deletes
Out[23]: [1, 2, 5, 6, 8, 9]
In [24]: np.delete(mytupList,indxList,axis=0).tolist() # Correct usage
Out[24]: [[1, 2], [5, 6]]
To retain the format of list of tuples, use map after deleting, like so -
map(tuple,np.delete(mytupList,indxList,axis=0))
Sample run -
In [16]: map(tuple,np.delete(mytupList,indxList,axis=0))
Out[16]: [(1, 2), (5, 6)]