If I change my selections to remove a folder from my backups, are they deleted at Enveloc?
No. One of the main benefits of backup is the ability to restore files which are no longer present on your computer. So, if you unchecked a folder in your selections list, the previous backups wouldn’t be touched. If you definitely want to remove something from your backup sets, use the “delete folders on server” feature on the maintenance tab. You may only delete entire folders, not individual files.