As far as I understand your the scenario is this.
You have backup of your primary SEPM.
You have reinstalled SEPM software. So currently there is no data present in the server.
If above is your scenario you can select option to clear all your previous data because
When you install and configure SEPM, it will create a database. This will have the only information what all you provided during the installation. But your backup will have all data from the fist installation to the backup date. Once you select the option to overwrite, all data which is present in the backup will be restored to the server. So you will not lose any data which is really needed.