Lost Notes

If a backup was created when you performed the sync, the notes should be in the backup.

First check to see if a backup was created. Launch iTunes and go to Edit>Preferences>Devices, you can see if there is a backup for your iPad in that window and see if the date and time correspond with your sync. If they do, try restoring for the backup.

Quit iTunes and then connect the iPad to your computer with the cable and iTunes should start up. If it doesn't launch on its own, start it yourself. If you are using iTunes 11 make sure that the sidebar is visible. If it isn't go to View>Show Sidebar at the top of the screen. If you can see the iPad under the devices heading, right click on the iPad name and then select restore from backup.

After the restore completes, sync with iTunes again.

Unfortunately, your assumption is correct. The notes are gone.