If you purchased Destiny for xb1 originally and got those pre-order items, you should be able to continue using them on xb1. If you purchased Destiny originally for 360, they do not transfer between console generations.
There is a small file necessary for the pre-order items (like collector's edition content), and if they aren't on your console, you will get that message. If you didn't delete anything, those files should still be there, though. Did you get a new xb1 console, or are you using the same one you originally played Destiny on last year?
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Did you try Kellogs10 suggestion to redownload those items through the Manage Games & Apps section? If you look at Destiny through there, it should show which related items you have downloaded previously. I know collector's edition and the pre-order sparrow show up for me when I look there. If it says "download" or "install" by those items, get those and then restart the game.