I myself am in a long distance relationship 4 years into my PhD also having a difficult time with both my project and sometimes my lab mates. When things get really bad I even consider quitting, my boyfriend (now fiance) would support me in whatever decision I made. He said ok well maybe you should look for jobs. I'd look and not see any that I would be interested in, and it would actually motivate me to make my own situation work. Sometimes it takes a lot of negative data to get something that would be suitable for a publication or thesis approval. I thought I had something good and then found another group that had published what my goal was, and then I about wanted to throw in the towel. So yes I'm stuck, and it's really hard not having someone to go home to that's comforting. But try to just be understanding and be empathetic to her situation. Maybe suggest a "facetime " date with a glass of wine or two and let her vent about it. Good luck!