When your github account has access to thousands of repositories on Github, it would appear that the client is timing out - the sync ultimately completes on the server, but the client bails before that happens. This is kinda a crappy user experience as the error presented is suboptimal:
λ nelson repos sync
[Post http://nelson.local:9000/v1/profile/sync: EOF]
Unable to synchronize repositories.
For some reason, the timeout is either not being honored on the client, or the server is cutting the connection but its not clear which.