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This frustrating behavior is the result of an intricacy of how the iPhone
deletes data. When you "delete" some kinds of items from the iPhone, they don't actually get deleted. Instead, they're marked for deletion by the operating system and hidden so that they appear deleted. But they're still on the phone.
How to Permanently Delete These Messages
If you want to truly and permanently delete messages from your iPhone, there are a few options:
1. Sync Regularly - Since syncing with iTunes is what actually erases items you've marked for deletion, sync regularly. If you delete an SMS on your iPhone and then sync your iPhone, the message really will be gone for good. (This method doesn't always work as you see)
2. Remove Messages from Spotlight Search - Your deleted SMS messages can't appear in a Spotlight search if Spotlight isn't looking for them in the first place. You can control what apps Spotlight searches in and which it ignores, so you can stop it from searching Messages. To do this:
From your home screen, tap Settings
Scroll about halfway down the screen and tap Spotlight Search
Scroll to the bottom of the screen and tap Messages to uncheck it.
Now, when you run a Spotlight search on your phone, SMS messages won't be included in the results.
3. Erase All Data or Restore to Factory Settings - These are fairly extreme steps, but they do solve the problem. Erasing all data on your iPhone does just what it sounds like: it erases everything stored in your iPhone's memory, including your text messages marked for deletion. Of course, it deletes your music, email, apps, and everything else, too, but it solves the problem.
These are the methods to permanently delete the messages from the phone (or hide from Spotlight)
I know this maybe not the answer you were looking to it is entirety but this is the best options available do to Apple flaw in iOS.Please reply back to me with any further questions BEFORE selecting a negative rating. I will answer your follow ups.