Yes, pretty much. When restoring from a jailbreak, it is always advisable to set it up in iTunes as a new device (and do not restore from your backup). A jailbreak can leave residual files that can cause problems down the road... especially if you rejailbreak.
So you must find external programs to sync your data. You can set these up through iTunes to backup your contacts, bookmarks, calendar, mail, etc. I use Nuevasync.com to sync my contacts and calendar, and Gmail doesn't need backing up really, so I'm set. You will lose notes and SMS unless you back them up via other means.
Check out Chronus on Cydia once you jailbreak. It will allow you to backup and email certain files to yourself than you can then use as a backup if you ever restore/rejailbreak.