Not sure what you mean by ”deployed using https://roots.io” but assuming that the site is set up using Bedrock, maybe this can help: Migration from bedrock to a normal install
I guess that once you have moved from Bedrock you can deploy it any way you prefer regardless of if the old way was using Trellis (https://roots.io/trellis/) or Bedrock-Capistrano (which, to my knowledge, are the two deploy methods built by the Roots team).