I found a way that actually works, note you will have to back up (a) Your Contacts (b) Photos (c) Notes (Voice Recordings), but this can easily be done through a program (and NO i do not work for the company) called iBackupbot. Please note you will have to GENERAL/RESET and select ERASE ALL CONTENT AND SETTINGS. This worked on iPhone 3GS, searched for at least 20 hours but REFUSED to give up, read SO MANY posts on the internet on how to DELETE THE SMS history in SPOTLIGHT SEARCH and nothing, NOT ONE program worked besides Wondershare Safeeraser which actually was the only program to pick up the 151 MSGS stored. Another reason I was unable to take this route and use this program is because Wondershare Safeeraser makes you dish out $40.00 to erase whatever those MSGS were.
I can only assume they were Spotlight Search history RELATED, because all my other messages had been deleted. Once again, I tried EVERY PROGRAM out there (iFunbox, Phone Cleaner, and a few more) and NOTHING, I REFUSED to Jailbreak my phone and get the ''ROOT ACCESS'' to the files which contained the SPOTLIGHT SEARCH HISTORY SMS, which I could never actually pinpoint WHICH ones they were being that there are NOT ONLY many different iPhones but IOS.
This worked for 3GS, IOS 6.1.6, but will probably work with 4 up to 5. And ONCE it's done, you will NOT see the SMS you THOUGHT were gone even if you tick MESSAGES in Spotlight Search. iBackupbot, did seem to have the option to RESTORE APPS, but I found it NON FUNCTIONAL, so if you do this, and it does work, make SURE you keep a record of the MOST IMPORTANT log in details of your apps so you can log back in after they are deleted. This was, the ONLY headache I encountered, but really after it was done, I realized I completed this process in less than one hour. I also took a screenshot of every Window on my iPhone 3GS (i do not have to pay this phone by the way, that's why I still use this older model), so I knew EXACTLY how to re-order the apps, internal or downloaded BACK to the way I had preferred.
I actually MESSED up my MSG system trying to get OTHER programs to delete the spotlight history, so I stumbled upon how to get rid of them PROPERLY and not purposefully. The reason I wanted to get rid of them so badly was because they contained MANY MANY texts to my EX GIRLFRIEND who's name I had no desire to keep on my phone.
Once you download iBackupbot (I used a CRCKD version by the way FULL VERSION), I made a backup, this has NOTHING to do with iTunes by the way which actually would not let me RESTORE 6.1.6 IOS even though it took more than 40 minutes to download it. Once you download iBackupbot, open it and make a backup copy of the contents of your phone, take your time and get familiar with the bar on the LEFT with all the folder. There is no need to open any of them however besides the USER INFORMATION MANAGER FOLDER which contains your CONTACTS / NOTES and also the only other folder which your CAMERA ROLL and VOICE MEMO'S under, I am referring to the EXPANDABLE folder right UNDER the USER NFORMATION MANAGER folder called MULTI MEDIA FILE MANAGER.
Please note based on my experience of trying and failing at a COMPLETE restore of the backup THINKING my SMS would be gone, I ended up making a PARTIAL restore which are easily select able (make sure the first box is checked, uncheck all others including MESSAGES besides the CONTACTS, CAMERA ROLL, VOICE MEMOS, AND NOTES. All you have to do is PLUG IN your device, and right click the folder (1) After a backup is made (2) After you ERASE AND RESET ALL CONTENT AND SETTINGS. PLEASE NOTE: You will have to set up your iPhone again, but it is easy, do not get frustrated, you will have to re-enter you Wifi (if you have one) and your Apple ID as well so MAKE SURE you have all that information. Once your phone is set up, tweak the setting as you had them before, then connect your iPhone back to iBackupbot and DO A PARTIAL RESTORE. If it makes you feel any easier about it, JUST IN CASE YOU ARE SCARED of losing all your CONTACTS / PHOTOS / NOTES & VOICE MEMOS, iBackupbot also gives you the option to IMPORT them all to your DESKTOP.
Lastly, even though my post is considerably long, I just want to say THIS WORKS, and it only took about one hour total. The RESTORE all APPS back to the phone DID NOT seem to work at all, but after I saw my CONTACTS / NOTES / VOICE MEMOS, AND CAMERAL ROLL were all there thanks to iBackupbot, I decided to download the 7 or 8 other Apps I had from the App Store (make sure you get all your login information for those apps if applicable, or else you may end up haggling to find out exactly what was the CORRECT user name and pass for all those apps that require logins). Lastly, make sure once you plug in your phone and open iBackupbot that you create a backup, that's all you should need, but again, just in case you are SCARED import all your files to your desktop.
I learned I never had to even import them back from the desktop, so I threw all those folders away (Except contacts in case I lose my phone..), but it's pretty easy. Before you attempt any of this I would also RECOMMEND you watch a Youtube video or three on how to CREATE BACKUPS using this program, called iBackupbot, I never felt I had too, it's pretty self explanatory once you become a little more familiar with that program, actually easier than I thought. PS: I am have ONLY written this all OUT because it was such a time consumer trying to find a program that worked, NONE OF THEM WORKED, not even iPhone clean, in fact I tried that program at least 5-6 times in DEEP SCAN mode and it still did not erase my SPOTLIGHT SEARCH HISTORY. There were one or two other programs I tried but they did NOT work at all, ANOTHER one I used was iPhone Browser, (a complete joke), Tenorshare iPhone Care Pro, the only other's I remember are I-Funbox, and iPhone Cleaner, Wondershare Safeeraser. I believe I may have tried Wondershare Dr.Phone, but it ALSO ended up being a waste of time. Good luck.
