I've read and followed your safe upgrade instruction and lost all notes and bookmarks for the 2nd time.  It's not possible for me and I presume countelss others to follow the upgrade instructions.  I cannot download any app or upgrade directly to my device.  When I go to update apps directly over the air on my iphone, the download and install begins and them I'm given the message" Cannot Install .... the application will be available next time you login to iTunes" or something to that effect.  Of course when you login to iTunes to install upgrades it does a complete sync and wipes out everything ..... VERY FRUSTRATING.

I see the new back up feature directly withing v2.0 and that's great but there still remains a problem with the way iTunes operates ....

Yes, I've heard from a few people who get the "Cannot install.. the application will be available the next time you log into iTunes."  I'm not sure what causes this, but I suspect it's a bug in the Apple App distribution mechanism.  I have faith they'll fix this eventually, though, as they're getting much, much better -- especially with the 2.1 iPhone firmware.  It's so much better!

Knowing that these rough spots exist, we added the backup and restore feature to our 2.0.0 Mantis software, and that helps a lot.  But it doesn't help you, unfortunately, because your trouble was before you could get to 2.0.0.

We're real sorry about this, but hope you hang in there.  This stuff is very new, and you're bound to run into more frustrations and woes until this platform (and our program) matures.  In the end, though, I believe it'll be worth it for you.