You messages (assuming you are referring to text/messages) are locally cached. You remove the cache by using iBackupbot http://www.icopybot.com/itunes-backup-manager.htm I haven't used it, but have heard a number of people give it good reviews.
"Backup your iPhone or iPad through iTunes. (Connect your iDevice to the PC/Mac, under the devices in iTunes, right click on your device and click on Backup Now; alternatively, you can also use the Back Up option from the Summary tab)
•From the sidepane, navigate to System Files > Mediadomain > Library > SMS > Attachments
•All the folders within Attachments are your Message cache containing all photos, video and media that you sent/received. Clear them out. At its best, delete all folders.
•Click on “Restore” so your iPhone is now restored to this backup.