In version 7.0.0.839, Veeam added full support for rotated media with all job types and backup modes removes the need of using additional scripting.

Remember to reboot the Veeam server after creating the registry entries.

These registry entries are put on the Veeam server where the console is installed.
HKLM\Software\Veeam\Veeam Backup and Replication\

ForceCreateMissingVBK (DWORD)
Enables support for rotated drives. With this functionality enabled, if any backup file from the latest full backup chain is missing (such as when the existing hard drive is replaced by another one), jobs will start the new backup chain and create the new full backup (instead of failing out).
Set to 1 to enable support for rotated drives.

ForceDeleteBackupFiles (DWORD)
Enables automatic cleanup of the backup repository from ALL existing files if any backup file from the latest full backup chain is missing (such as when the existing hard drive is replaced by the hard drive brought back from offsite location, and containing some older backup files).

Set to 3 to make the job delete the entire contents of the backup job’s folder only.
Set to 5 to make the job delete the entire contents of the root backup repository folder, thus potentially deleting any files belonging to other jobs along. Note that if backup repository points at the volumes root folder, the entire volume’s contents are erased.