"Backup files created with Veeam Endpoint Backup are removed automatically according to the retention policy settings. However, you can also remove backup files manually if necessary.
Always delete the whole backup chain from the target location. If you delete a full backup file or individual incremental backup file from the backup chain, the chain will be broken, and Veeam Endpoint Backup will fail to perform the scheduled backup next time.
If you remove the whole backup chain from the target location, during the next backup job session, Veeam Endpoint Backup will produce a new full backup. All subsequent backups will be incremental."
I pulled that from the User guide, did you try removing all the backups and letting it run a fresh full?