Currently every HDF5 file produced with jsontoh5 will use the latest file format, H5F_LIBVER_LATEST: https://github.com/HDFGroup/hdf5-json/blob/develop/h5json/hdf5db.py#L167. This creates a problem for software that still does not use, or never will, the latest version of the HDF5 library.

jsontoh5 should have something like --libver option with either earliest or latest for values. I don't think that h5py yet supports all the new options described here: https://portal.hdfgroup.org/display/HDF5/H5P_SET_LIBVER_BOUNDS.