If you are using the full backup + incremental backup scheme to backup your folder/server and you restore your full backup + incremental backups, you will find that your resultant folder/server will contain all the files that has been previously deleted. This is because incremental backups do not keep track of deleted files.
To keep track of deleted files, you would need the Advanced Disk-Based Option (ADBO) which is a payable option. In BE 2012, ADBO is part of the Enterprise Server Option licencing bundle. ADBO enables you to do True Image Backups which will track deleted files. When you do a restore from a Full Image backup, you will not get back your deleted files.
True Image Backups is also needed for another ADBO feature called Synthetic Backup. Synthetic Backup allows you to amalgamate your full backup and the subsequent incremental backups into a full backup without the need to access the server that the files are backed up from.
For earlier versions of BE, you do a True Image Backup by selecting the following job property
For BE 2012, it is not so obvious how you do a True Image Backup.
If you want to do synthetic backups, then you would select synthetic backup when you create a backup job. This will give you a set of jobs; full backup, incremental backup and synthetic backup. When you select synthetic backup, True Image backups will be done for the full and incremental backups.
What if you want to do True Image backups, but not synthetic backups?
You will select a normal backup and then change the backup method to the Use Catalog method
The explanation for the Use Catalog backup method is
Using catalogsBackup Exec uses the Windows Change Journal to determine if a file has changed since the last time it was backed up. Backup Exec compares path names, modified times, deleted and renamed files and folders, and other attributes. If the Change Journal is not available, Backup Exec compares the file information to previous catalogs to determine if it has changed. This method is required for synthetic backups and true image restore. It is the most thorough method, but it takes more time to run.