pkgsrc doesn’t officially support re-bootstrapping once it’s been installed (ie updating the core packages by doing a fresh bootstrap). There is a way to force one by removing a few core packages first though:
pkg_delete -ff bootstrap-mk-files bmake tnftp pax pkg_install
cd /usr/pkgsrc/bootstrap
./bootstrap

As long as the fresh bootstrap is done using the same parameters as used originally (prefix, database directory, etc), everything should work as before.

I tested this a short while ago on an OS X 10.5 system using a pkgsrc -current tree and it worked perfectly.