How do you deploy (using Roots Trellis) to a domain that has CloudFlare proxying it?

I built a site using Roots' Trellis that now uses CloudFlare, thus proxying traffic. Which, understandably, prevents Trellis from deploying via MyExample.com.

I’m aware I can connect via IP or an un-proxied CName (Ex. ssh.MyExample.com). But I am unclear about which file(s) I edit in Trellis so the deploy uses the IP or un-proxied domain.

It seems that editing the /hosts/production file would do the trick, but the rest of the Roots ecosystem depends on the values in these files I'm afraid that re-running the deploy with corrupt the server. This has been my experience with similar issues in the past.

Can anyone confirm the steps to achieve this?

1. Edit /trellis/hosts/production at lines 5 and 8, below [production] and [web] and update it with the un-proxied domain (ex. ssh.myexample.com).
2. Save, and Git commit your change.
3. Navigate to the /trellis/ directory and run your deploy using the proxied domain. Ex. ./bin/deploy.sh production myexample.com