How to sync iPhone safely without loosing data after reinstall of OS X

Hello,
This might be a very basic question! I recently erased and reinstalled Mountain Lion on my 15" MacBook Pro. I have full backup on an external drive. My iTunes library was not very well organized, I am planning to rebuild iTunes library. My guess is if I connect and sync my iPhone 4 (iOS 6) to iTunes, it will erase everything from phone? Is that true?
I do not want to loose Notes, Apps and other settings from phone, Notes are only on the phone (and lots of them), not on iCloud. Music, I dont care much, I will sync as I add more music to iTunes library. Also, I have an iPad (with iOS 5) which I want to sync to new library as well.
How should I go about it?
Thanks much in advance!
Cheers

Read here:
https://discussions.apple.com/docs/DOC-3141

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http://www.everymac.com/systems/apple/ipad/ipad-troubleshooting-repair-faq/ipad- how-to-unlock-open-forgot-code-passcode-password-login.html
iOS: Device disabled after entering wrong passcode
http://support.apple.com/kb/ht1212
How can I unlock my iPad if I forgot the passcode?
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http://ipod.about.com/od/iphonetroubleshooting/a/Iphone-Recovery-Mode.htm
You may have to do this several times.
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~~~~~~~~~~~~~
‘iPad is disabled’ fix without resetting using iTunes
Today I met my match with an iPad that had a passcode entered too many times, resulting in it displaying the message ‘iPad is disabled – Connect to iTunes’. This was a student iPad and since they use Notability for most of their work there was a chance that her files were not all backed up to the cloud. I really wanted to just re-activate the iPad instead of totally resetting it back to our default image.
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Through some trial and error (and a little sheer luck), I was able to reactivate the iPad without loosing any data. Note, this will only work on the computer it last synced with. Here’s how:
1. Configurator is useless in reactivating a locked iPad. You will only be able to completely reformat the iPad using Configurator. If that’s ok with you, go for it – otherwise don’t waste your time trying to figure it out.
2. Open iTunes with the iPad disconnected.
3. Connect the iPad to the computer and wait for it to show up in the devices section in iTunes.
4. Click on the iPad name when it appears and you will be given the option to restore a backup or setup as a new iPad (since it is locked).
5. Click ‘Setup as new iPad’ and then click restore.
6. The iPad will start backing up before it does the full restore and sync. CANCEL THE BACKUP IMMEDIATELY. You do this by clicking the small x in the status window in iTunes.
7. When the backup cancels, it immediately starts syncing – cancel this as well using the same small x in the iTunes status window.
8. The first stage in the restore process unlocks the iPad, you are basically just canceling out the restore process as soon as it reactivates the iPad.
If done correctly, you will experience no data loss and the result will be a reactivated iPad. I have now tried this with about 5 iPads that were locked identically by students and each time it worked like a charm.
~~~~~~~~~~~~~
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 Cheers, Tom

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How to sync iPhone safely without loosing data after reinstall of OS X

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