Yes -- you can backup your bookmarks, notes, and highlights at any time using the "Backup" button. In 4.0, incidentally, this button also backs up your Daily Reading Log as well.
As far as your purchases go: yes, we keep track of your purchases. We've taken great strides to make sure things go really smoothly for you if you ever need to reload your iPhone or iPod Touch. It's really very, very easy.
Say you need to do a factory reset and wipe out your entire iPhone. You will need to download and install Mantis Bible Study again. (The easiest way to do this is to tap on App Store, search for Mantis Bible, then install it.)
Once you re-install Mantis, as soon as you start it up, it should go get your list of purchases from our server (after about 10 seconds or so). Just go to your bookshelf and you'll see your purchases as "Ready to Download".
Now, if you should have to return your phone to Apple for a replacement -- just contact us via our Support page. We'll reset your user name so you can type it in on the Settings page on the new phone. Your purchases will then show up again -- no problem.