With each Slack account you can only back up one Slack workspace: In Slack you can access multiple workspaces with the same Slack account, but each API connection can only be linked to one workspace. For this reason you can only select one workspace when adding Slack as a backup to your account:

If you wish to back up multiple Slack workspaces with the same Pro Backup account, you need to invite a different Slack account for each workspace that you would like to back up.

To do so, follow these steps: