When removing unneeded packages from a (read-only) rootfs
during rootfs creation, alternative symlinks from those
packages may or may not be removed.

The reason is as follows:

update-alternatives(-native) is used during package
installation as part of the image creation. It uses
a database which contains entries for all the
alternative symlinks possible, and the -native version
uses the target's database by means of $OPKG_OFFLINE_ROOT,
i.e. the rootfs we're in the process of creating.

Once the rootfs has been created, OE removes certain
packages because we have a read-only rootfs - in
particular ROOTFS_RO_UNNEEDED which includes
VIRTUAL-RUNTIME_update-alternatives, i.e. the
update-alternatives. Recently, a change was made in
OE, where uninstallation of update-alternatives from the
rootfs causes removal of its database, too, to save space
(700KiB (uncompressed) in a busybox system)
  b24a63d71b517af701dfedbc7f7b541d25af708f
  http://git.openembedded.org/openembedded-core/commit/meta/recipes-devtools/opkg-utils/opkg-utils_git.bb?id=b24a63d71b517af701dfedbc7f7b541d25af708f

Following from that, if update-alternatives is removed
from the target file system, update-alternatives-native
has no database anymore, meaning it can't manage any of
the alternative symlinks anymore.

Because the order of packages to uninstall is
non-deterministic, and update-alternatives could well
be removed before any packages that use the mechanism
provided, sometimes the extra symlinks are removed,
sometimes not.