[@Jacob] Dear Jacob,
What you are describing is called “Disaster Recovery”, and Genie Timeline (GTL) provides this feature.
Making a Disaster Recovery from GTL backup requires that you remove your old Windows installation (Formatting the HD), and then to make the recovery as described in the following article:
This way, only the files which were on your HD on that selected restore point will be restored.
Robin Scott / Genie9 Team