You need to force a Backup job or Backup Copy job to create a new backupset.
The backup files have been removed from disk, and you need to remove the file references from Veeam's configuration database.
Note: Please ensure that the destination will have the space needed to start a new backup set.
Steps on removing backup files from configuration can be found here:
Note: If the Backup Set that is being removed is for a Backup Copy job, make sure to Disable the Backup Copy job first. If this is not done, the "Remove from configuration" option will be greyed out and unavailable.
Run the job, a new backup set will be started.