Deleting data from a HDF5 file requires repacking of the master file. Since we use large sub-db files (measurement data), separate HDF5 datafiles are externally linked into the masterfile. As the linked files take up little space you could argue if a repack will be necessary.
As HDF5 database can get corrupted, what is the procedure to remove the externally linked databases (h5py.ExternalLink) correctly from the master HDF5 db file?
The ExternalLink object behaves like other objects (groups and datasets). So, you can use del and reference the file/link object.
For example, if you have an External Link named ['/my_linked_ds'] you can delete like this:
h5f = h5py.File('yourfile.h5', 'r+')
del (h5f['/my_linked_ds'])
h5f.close()