Trying to backup an iPhone 3gs so we can update the iOS. Old computer does not appear to back up contacts and notes (there are many). Is there a way to make sure they are backed up?

Also, everytime we sync, emails delete from the iPhone. We don't want them to. Is there a setting to prevent this from happening?

Contacts are not part of the backup. Those should be synced with a compatible address book on your computer. Notes can sync with a mail account.
No idea what you mean about emails deleting from the phone when you sync. E-mail messages are not synced with anything but the mail server. Only account information is synced.

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