pki: upgrade: do not overwrite apache certificate and key

Fix missing existence condition before duplicate the apache certificate
and key.

This will overwrite 3rd party certificate (if installed) at upgrade from
3.2 to more recent 3.2.

Change-Id: I638e9193fdda7ca9a88313ba1890e9c1a76179af
Signed-off-by: Alon Bar-Lev <alonbl@redhat.com>
Bug-Url: https://bugzilla.redhat.com/show_bug.cgi?id=969755