First: go into iTunes, Preferences, the Devices tab and turn off auto syncing. This will keep iTunes from overwriting your last backup, just in case it's got your notes in it.
Before we go into backups though, lest check another possibility.
Connect your iPad to your computer, open iTunes, and select your iPad from the list of Devices. Now choose the Info tab at the top.
Scroll down until you can see where it offers you the ability to sync notes. Is it selected? If so, you're probably out of luck.
Select it, and note what app, or apps, it says it can sync your notes with. Now deselect it and go to those apps to see if your missing notes are there. If they are, go ahead and turn the sync back on and do the sync.
The only other possibility is the backup. If you have not backed up (synced) the iPad since loosing the notes they may be in the backup file. Unfortunately the only way to find out is to restore from the backup.
Open Preferences in iTunes and go to the Devices tab. Look at the date of the backup for your iPad and see if it is before your update. If so, you've got a good shot at getting the notes back.
If you choose to restore from the backup, you will lose all other documents you've updated or added since the backup. So save or transfer them somewhere safe first. Be thorough. You may also loose you place in games, system settings you've made, pictures in the camera role, imported, or saved pics, and other adjustments.
When you are sure you've not going to lose anything important, go ahead and right click on the iPad and choose Restore from Backup.
It works, or it doesn't.
