Scarlet, I sympathise with your situation. I met my fiancee (an American international student) at university but she was skipped year 1, meaning she finished a year before me. As with you, the thought that we'd be apart for at least a year popped up every now and then but it seemed quite distant. Of course the time flew by and before we knew it it was time for her to leave. It's been almost 16 months since we last seen each other and it has been VERY difficult for both of us, but we will be getting married later this year! In fact we both wish now that we had just married before she had to leave, though I think the '3-years' issue will mean that's not an option in your case.
I can't overstate how difficult the time apart will be, but my feeling is that if what you have is real, then it will endure and survive hardship.