Prune removes all the versions but the last, not the current one.
For exemple, I have old sources on my laptop and use the 2.6.17-r4, which is
not the last (2.6.17-r7) :

ptigris ~ # emerge -pP gentoo-sources

>>> These are the packages that would be unmerged:

 sys-kernel/gentoo-sources
    selected: 2.6.16-r9 2.6.16-r12 2.6.16-r13 2.6.17-r4
   protected: 2.6.17-r7
     omitted: none

>>> 'Selected' packages are slated for removal.
>>> 'Protected' and 'omitted' packages will not be removed.

It wants to remove the one I use, so I want use this command, I must
recompile the last one with my .config file.