So after some faffing about I think I finally managed to resovle it.
I used fly ssh console to access the db instance.
I then spent a while figuring out what params I needed to pass into stolonctl to get the status:
stolonctl status --cluster-name $FLY_APP --store-backend consul --store-url $FLY_CONSUL_URL
Then I could identify and remove the unhealthy (Removed) keepers and use stolonctl removekeeper
This appears to have resolved the issue but took an unnecessarily long time to figure out.