It very easy to replace bookmarks stored your computer in safari or internet explorer to your iPhone but this way iTunes will delete all the bookmarks stored in the safari browser on your iPhone and overwrite with all the bookmarks on your phone.
But what if you want to backup all your safari bookmarks so that you can restore them on your iPhone by syncing next time after firmware upgrade. It was some what different case with me, as I want to backup all the safari bookmarks on my iPhone so that I can restore them back after jail breaking my iPhone 3g.
Lets see how can you backup all your iPhone safari bookmarks on your computer browser including Safari or Internet Explorer
1. Connect your iPhone with data cable and run iTunes
2. Now, select your iPhone and click the Info tab, select Sync Bookmarks With Safari or Internet Explorer
Note: Please backup all your existing bookmarks in the browser you select for the sync, to be on the safer side. as syncing might delete your computer browser bookmarks.
3. Make sure that Bookmarks should be unchecked under Advanced
4. Click Apply button after setting all these options, and it will start syncing your iPhone safari bookmarks
5. After some time it will ask you to allow changes due to some of the bookmarks copied from iPhone Safari Browser, click allow to let it proceed and copy the iPhone safari bookmarks to your computer browser.
Please Note: The over all process of syncing the bookmarks in between iPhone and your computer is a two way sync, so it might delete your iphone or ipod touch bookmarks if you dont read the sync alert properly. So as you can see in the image below if it says that it will change some percent of bookmarks on your computer browser and it is adding or deleting the bookmarks on your computer then only click the button Allow
Else you might end up deleting your bookmarks on your iphone or ipod touch
That’s it, After sync is complete you will see your iPhone safari bookmarks in the respective browser you choose, in my case it was safari computer browser.
Disclaimer: Please use the above procedure at your own risk, and read it properly word by word before applying. I am not responsible for any damage caused to your iphone or ipod touch following this procedure