As you may have noticed, Decipher Backup Repair doesn't edit the original backup while doing its repairs. Instead, we make a clone of the original backup (conserving hard drive space as much as possible) with the adjustments.
Here are the instructions from Apple about how to delete backups in iTunes. The repaired backups are named starting with "Decipher Repaired" or "Decipher Advanced Repaired" to help you identify them. Alternatively, you can open Decipher Backup Repair and click the "Delete this Backup" button to delete a repaired backup.
If you restored the repaired backup to the same iPhone device that originally made the broken backup, you may also want to "Archive" the original backup in iTunes so that iTunes doesn't try to update the old broken backup as it makes new incremental backups.