Greetings Degee,
Thanks for using Apple Support Communities.
I see that you have synced your iPhone with iTunes, and then after that your Safari bookmarks are missing. I can imagine that it's concerning to not have all of your favorites after you sync. Let's get this sorted out.
Syncing your iPhone with iTunes shouldn't have any affect on your bookmarks. iTunes can't sync certain content, including mail accounts, notes, or bookmarks. I would advise to close the Safari app, and then reopen to see if the bookmarks reappear. And also to give the iPhone a fresh restart. These articles will help:
Force an app to close on your iPhone, iPad, or iPod touch
Restart your iPhone, iPad, or iPod touch
If you are using iCloud Bookmarks, use Get help using iCloud Bookmarks and Reading List​, specifically, this section:
iPhone, iPad, iPod touch
After each step, check to see if the issue still exists.
Turn on Bookmarks and update your device
Check your Internet connection
- Open Safari and go to www.apple.com. If you can't connect to the Internet, your iCloud Bookmarks and Reading List won't update in the Safari app. Get help with your Internet connection.
- Open a secure website from your iOS device to see if you can access ports 80 and 443. Safari requires access to port 443 to push updates between iCloud and your devices.
Check your account details
Tap Settings > iCloud and make sure you're signed in with the same Apple ID that you're using on your other supported devices.
Restart Safari
Close and restart the Safari app on your iOS device.
In iOS 7 or later:
- Double-click the Home button to see your open apps.
- Find the Safari preview screen and swipe it up to close the app.
- Press the Home button to return to your Home screen.
- Wait a minute, then reopen the Safari app.
Turn off iCloud Bookmarks and turn it back on
- Tap Settings > iCloud.
- Turn off Safari.
- You can choose Delete from My [device] if your data exists on one or more of your computers. Otherwise, choose Keep on My [device].
- Wait a few minutes, then turn on Safari again.
Best Regards.