Story has reset and I lost my ship bookmarks and Teleport bookmarks

I'm pretty sure my files are corrupted some how, but here is what happened. I was playing 1.3 for about 2 days when my computer completely froze; so I hard reset it. When I started Starbound again after my computer booted up, my character was gone. So I closed Starbound, opened it again and my character was there!! (Maybe the cloud data took a while to catch up). So I open my character and I have all my stuff, crew, items stored in my ship; everything looks good. But all of my bookmarks and Teleport bookmarks are gone. I had to find a low threat planet, get 20 core fragments to activate the warp gate to the outpost again. Once I got to the outpost, I realize that the story had been reset; all the shops are closed, I have to start the mech quests over, and the gate to the final boss is closed. But it's also weird, because (What's his face's) museum is still full of the stuff you scan and collect through out the story. It's like all my items and stuff are saved and I'm still a high level, but the story is back to the beginning.

If anyone knows how to possibly fix this, (or at least tell me the coordinates to the Gomeisa Veil solar system) it would be much appreciated. (Gomeisa Veil is the system with my settlers and collection of stuff)

 

Here it is. I don't think you need the ship file, but I threw it in anyway.