I'm trying to convert all the values that are zero to one, as referenced in this question. Using the indexing method has no effect on the matrix though.

How would I change all the 0's in my matrix to -1?
Your boolean indexing is failing because new_train_data is currently a matrix of strings (dtype='|S3'), not floating point numbers!
You can cast the matrix to dtype=np.float64 to convert it to floats, then use boolean indexing to assign a value of -1 to all elements that are equal to 0.0:
new_training_data = new_training_data.astype(np.float64)
new_training_data[new_training_data == 0] = -1