correct me if im wrong but, why would you loose your notes and bookmarks? jailbreaking doesn't do anything to delete anything you arlready have. its just like a regular restore it will back up everything youve backed up prior to jailbreaking
But in the process to pwn your iPhone you choose a custom built IPSW file, and none* of the guides I've read (I've found 4 so far) talk about what to do when you have to decide between setting up the phone as new or from a backup. I thought you were supposed to set it up as new.
*Cheese! 9 months or so of jailbreaking and none of the guides have EVER EVER EVER discussed this issue.
When I updated from 1.1.4 to 2.0 and Jailbroke and Unlocked I lost my notes and bookmarks.
EDIT: Now I remember why I lost my stuff, my phone was synced to my desk top in the US and now I am in Iraq with a new laptop and it would not let me back up because it was synced to a different library.
If you backup your phone with iTunes before jailbreaking it, you should be able to restore from that backup (not a Restore to update the firmware) and get your stuff back. I went from 1.1.4 to 2.0, then jailbroke 2.0, then ended up going BACK to 1.1.4, then got a 3G and through all of that, I still have my original Notes and Bookmarks on my new phone.
iTunes keeps a set of backups that you can restore from anytime you do anything like a firmware Restore or Update.