I would like to extend the very nice answer by Jens with the exact procedure to delete all density entries but the very last one from the cdn.hdf file. First: As a general information on what is stored in the cdn.hdf file you can invoke fleur with the "-info" command line option. If there are many density entries listed in the output you can considerably reduce the sice of the file with this procedure (though it is not proportional because there is also some data stored that is independent of individual density entries).

To delete all old entries which are not needed if you don't explicitly tell Fleur to use them you can invoke Fleur (let us assume that the name of the executable is fleur_MPI) with

fleur_MPI -delden allbutlast
 
 

After doing that the respective entries are not listed any more but the file size is not yet reduced. For the reduction of the file size an external tool has to be used. The HDF5 library comes with the tool h5repack to do that. The exact procedure is described in the Fleur output when invoking the program with the "-delden" option. In detail one has to execute thefollowing two commands:

h5repack -i cdn.hdf -o cdn-packed.hdf
mv cdn-packed.hdf cdn.hdf
 
 

After this the file size is reduced. Note that there are also more sophisticated options for the "-delden" mode allowing you to only delete certain density entries or a user defined range of such entries.

We typically store all entries to allow the user to restart Fleur with slightly changed parameters, e.g., for the mixing procedure, from an intermediate density. Sometimes it is good to have this option if a system does not converge as expected.