I came out of hiding just to give my two cents, sorry if its LONG. Unfortunately, PCOS and all the various issues that can accompany it, are issues I'm too familiar with.
Condensed story is, grew up an athlete, played soccer from age of 5 til high school competitively; and played other sports too, club volleyball & tennis. I was an active kid. But I was always muscular fat, thick, curvy (large chest, booty etc.) not flubberly fat, only fat around the abdomen (no one understood how that could have been with the level of training I was doing). It all began around puberty, so I always had irregular periods. I trained like any competitive athlete; but back then, it was a lot of cardio and diet wise a lot of refined carbs. This lead to a lot of over-training & distorted eating i.e. near starvation because of the mantra train more, eat less (doesn't work for people who have hormone problems). A lot of yo-yoing, going to experts (traditional nutritionist) that didn't know anything about PCOS (it wasn't even in the realm of thought), so no diagnosis all throughout high school.
Fast forward, started really lifting in college, but was still not honed in on diet, at least, the right diet (nutrition) for my unique issues. I started a traditional bodybuilding training and dieting (clean eating). I saw some results, I started this around the same time, I began here on T-Nation. But with that came a lot of supplementation that I should have probably been more knowledgeable about before beginning (i.e. fat burners, pre-workouts etc.)
Anyways, I transitioned from Clean Eating to Anabolic Diet, Velocity for its intended purpose and then to Keto-clean. All worked in their own way, but I always hit a wall. I realized that I got the best results when I watched (refined) carbs (near ketosis or in ketosis) but if truthful, still not eating enough but training a lot. About 4 years ago I was at my worst, stressful job situation & family financial issues, back injury (pinched nerve) from a job related injury, I hit the wall hard. I started seeing really bad symptoms besides the irregular periods: fatigue, losing/thinning hair along hairline,scalp psoriasis, uncontrollable weight gain (highest weight), male-pattern hair growth (chin etc.)
The last two years, I cut everything out, all supplementation. My adrenals were probably also shot from all the caffeine from abusing pre-workouts & fat burners. I went strict Paleo, mostly because I believe the body knows how to heal itself and when you have hormonal problems not eating food products laden with chemicals and hormones helps with not stressing the already stressed out system. In my opinion, its the best possible way to eat for my issues and respectively PCOS. I started seeing a Dr. who understood PCOS, she finally diagnosed me. I found out I was hypothyroid and insulin resistant. She put me on Cytomel & Metformin. Within that year, my hormones were restored and all my symptoms subsided or are gone, periods are back or finally regular without progesterone and I lost 40lbs (which was a huge accomplishment, because just looking at a refined carb made me gain 5lbs overnight), still maintained muscle and built on strength (I'll never have a problem with that) through the whole process. Currently, I am a 80/20 Paleo (so still no refined carbs, actually I have a wheat allergy and lactose intolerant, but I'll have a dirty carb up when I get too low), also eat the right amount of calories for my body & activity. I do a body part split 3-4x a week HEAVY lifts routine, either 1 HIIT or 1 LONG CARDIO a week (cardio very sparingly, this has to do with not stressing the system). In the last two months, I lost another 20lbs and expect to be at "ideal" by mid May early June 2015 that is if my body doesn't plateau (but that's a normal part of fat loss). I just reintroduced supplementation about 2 months ago (beef base protein powder and pre-workout sparingly). I expect to be off everything and not have any issues with PCOS ever.
I hope this helps. Its been a long journey, and I'm hoping by sharing this. Your girlfriend will not have to suffer as long as I did. I chronicled everything from the last two years on my blog: http://fitrosed.blogspot.com/