Yes, to be on the safe side, you'll need to have that data and files somewhere in another place or in iTunes.
I'm not sure, but they may stay with the app when you do a "transfer purchase" and then a full backup. I had some pictures in the Photos app and some pictures and files in another app (iFiles) and when I finished the jail break, those files were still there (in fact, I had to check just now because I forgot about them when I was copying and backing up ... Whew! They're still there...). I've just looked through various apps I have and all the data that was there before is still there. This includes a book I downloaded from the App Store and had in the iBooks app (and the PDFs, also).
So, while I would not (can not?) say that a back up WILL preserve your data - I can tell you that mine was all there when I "restored from backup" after doing the jail break. I still recommend you save your important data elsewhere, just in case, even if that means you have to do a bunch of e-mailing.
For music or audio books, I would suggest finding a third party program so that you can get them off the iPad and back into iTunes. Because you can't do a sync or "transfer purchases" to put them into iTunes if they are not already there. With iTunes, it's one way: from iTunes to the iPad.
Hopefully, there's some useful info in what I typed.
Good luck.
Marilyn