Is it possible to rollback changes through the SDF CLI? I've had a look around - a lot of talk about it but I couldn't find any examples.

Yes. This is a downside of an account customization project. SuiteApp projects don't have this downside. With a SuiteApp project, checkout a previous version of your project from source control and deploy it, SDF will update all existing objects and remove any objects that are no longer part of your project. Super cool. If it weren't for the annual dev fee to deploy SuiteApp projects, this would be the way to go.

Thanks, Mike. I guess I'll need to look into SuiteApp projects more - are they structured in the same way as an account customization project? Are there any other draw backs outside of the annual fee you mentioned?

No structural differences in the project. In the UI, there is a "App ID" field on each customization object. This is used to identify which customizations are part of your project so SDF knows which customizations should/can be removed, if necessary. This field is populated automatically when you deploy with SDF, but can be manually edited as well.