Playing on PC.
So I went to go do some bounties and stuff for Spider and noticed that Petra wasn't in the corner. I thought this was a glitch so I went to go do Spider's bounties and other stuff for maybe 2+ hours. I go back, and she's still gone. I did some experimenting and I put a tracking thing on her and walked out of the area to see what would happen. The marker pointed to inside of Spider's Safehouse. Right as I enter the area, it shows she's there for around half a second but then vanishes. No clue what caused this to happen.
I had this happen when I first ran through the Forsaken campaign. What fixed it for me was going to orbit and then go back to the Tangled Shore. It might take a couple orbits to fix it. Also, if you’re in a fireteam when this happens try it solo.