I can't remember if I read this within the app or on a website (or if I'm just confused), but I think the "Archive" feature just deletes it from the iPad. I'm on the fence... I wish there was a way to back-up copies in iTunes so if I ever have to restore iOS I won't have to redownload the magazines... but I also think that as long as the magazines are available to be re-downloaded, it's not a terrible inconvenience.
I think the Zinio magazine app lets you backup the magazines to iTunes.