For the usrmerge some programs need to drop the master link in eg /bin and a link in /usr/bin as master instead. update-alternative deletes such links if the one in /usr was a slave before though.

# /usr/sbin/update-alternatives --install /bin/foo foo /usr/bin/true 15 --slave /usr/bin/foo usr-bin-foo /usr/bin/true
   update-alternatives: using /usr/bin/true to provide /bin/foo (foo) in auto mode
# /usr/sbin/update-alternatives --install /usr/bin/foo foo /usr/bin/true 15
   update-alternatives: renaming foo link from /bin/foo to /usr/bin/foo
   update-alternatives: warning: forcing reinstallation of alternative /usr/bin/true because link group foo is broken
# l {/usr,}/bin/foo
   /usr/bin/ls: cannot access '/usr/bin/foo': No such file or directory
   /usr/bin/ls: cannot access '/bin/foo': No such file or directory