For instances of octopub (e.g. http://fsa-octopub.herokuapp.com/) we indeed ought to have a migration script. @caiwilliamson has been thinking about that.
For octopub.io, we made the decision to not port everything wholesale, as most of the data were tests and experiments, and there was a lot of cruft in there. Instead we chose to keep the old octopub instance alive for the next ~ 6 months and proactively start a conversation with people who we know have been actively using old-octopub and understand whether/why they would need to migrate to the new system... as well as make sure they understand that the instance is provided as-is, with no official support, that we may take it in strange directions through some of our experiments, etc.
For both: datasets already published on github will of course stay there, regardless of what happens to octopub, and be manageable from there.
Old datasets do not appear to have been migrated. See:
https://twitter.com/Ox1Digital/status/1021996431471722496