Good luck! =)
I've heard that something in the cert renewal process doesn't like it when the Pump.io process is running and having control of the 443 port, or something like that.
Maybe something to check...
@jankusanagi@identi.ca looks like there's a manual option or a webroot method that might work without restarting your server. Or maybe the Apache plugin would work of you're running pump in the proxy configuration. https://certbot.eff.org/docs/using.html