90m day visa, exit and return to HK

My grilfriend is coming on holiday to HK 20th April, She will stay for 2 week on a holiday. She will then return home to europe for 5 weeks. She will then come back to HK and re-enter, around 15th Junhe. I can see that she can re-enter HK in early June but how many days can she then remain. On her second entry she wants to stay with me in HK from mid June to mid September, this is 3 months. If she returns 15th June and they don't give her a new visa entry stamp for 3 months, can she go to Macua and get another 3 months visa stamp after the 1st 3 month visa stamp has expired. How does it work ?