There are dozens, if not trillons, of guides out there showing us how to use reprepro to create and add packages to a deb repository. Much as the documentation for their end user package manager bretherin however, there's scant info anywhere about how to update an already existing package to a newer version.
To start, when you add a package you do this:
reprepro -b /repopath includedeb wheezy package_1.0.0_arch.deb
To update, you don't need to delete the previous, you just add the next version:
reprepro -b /srv/repopath includedeb wheezy package_1.0.1_arch.deb