Thank you all for your responses, I wasn't expecting them so fast. I already looked up the information on the digital upgrade, and contacted PSN support before posting on here and didn't get any helpful answers. I was hoping that it would be a different situation, given I only wanted 1 version instead of both. That said, I only asked PlayStation Support if I could swap out the PS4 version for the PS3 version. I noticed that one of Playstation's refund policies is if you purchased content for a system you don't own. Having played it on a system that I didn't own and no longer have access to, would this apply to me? And is there any kind of support from Bungie I can or should contact on this matter? As I said, I'm barely into the game right now and really don't want to stop playing because of this.

Practically you don't own the system anymore, so they should make a refund to your account. Also the best place for support are the #Help forums there are Mentors, Bungie employees and a lot of helpful people willing to give some advice. It shouldn't hurt trying to contact PlayStation Support again and tell them your case.

I've tried getting in contact with them, but they're pretty much been ignoring all of my methods of contact (won't let me access live chat, no answers on twitter, and mods on support forums do nothing other than refer me to these other contact options).This probably won't be getting sorted out anytime soon.