I originally Pre-Ordered the Collector's Edition - though not the deluxe - version for PS3 as that was all I had at the time and wasn't thinking of upgrading. However, I recently upgraded since there was a good deal in my area and I picked up a regular copy of Destiny for the PS4.
The problem I am now having is that - if I play on the PS3 - all is well and good and right with the world. If, however, I switch to the PS4 - where I normally play now - I find that all of my special items from the Collector's Edition - which should be tied to my account - are now telling me that they require the collector's edition purchase.
While I'm not too worried about the shader or the ship or such, the DLC Expansion Pass that I had as part of that is something that I would still like to know is applied to my account as it is something that I paid for.
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The items only work on te system they were purchased for. The expansion pass will be fine on both systems. See destiny's upgrade site for more detail: http://www.destinythegame.com/digital-upgrade