How to overwrite array inside h5 file using h5py

You want to assign values, not create a dataset:

f1 = h5py.File(file_name, 'r+')     # open the file
data = f1['meas/frame1/data']       # load the data
data[...] = X1                      # assign new values to data
f1.close()                          # close the file

To confirm the changes were properly made and saved:

f1 = h5py.File(file_name, 'r')
np.allclose(f1['meas/frame1/data'].value, X1)
#True