I ran into problems with changing/adding repositories as well. I now believe my problems were related to unclarity in the documentation. The wiki merely says "Repositories can be declared in a file stored in /etc/xbps.d with a simple format," giving the impression that the naming of the file could be arbitrary. So I named the file I put there in such a way as I could easily identifiy it, not bothering with things like suffixes. Yet the repository I'd added in that files using the repository= syntax was not being picked up.
Looking over the wiki article again, I noted the example "echo 'repository=http://my.domain.com/repository' > /etc/xbps.d/my-remote-repo.conf, and decided perhaps the file naming was not supposed to be totally arbitrary, but that a certain suffix--namely the .conf suffix--was required to be appended to the file name. When I added that suffix to the file I'd created, the system then picked up on the new repository I'd stipulated.