On a break

So my girlfriend and I have been in a really happy relationship for just over a year. We've made each other feel like more complete people, had some amazing days together and talked about our futures together till recently and have only really argued when drunk.
But a couple days ago she asked for a break from me so she could understand why her feelings had changed and what was going wrong so we could fix things and start again. I've agreed to this and we've said that there won't be anyone else whilst on this break and we've set a time on it.
The past three-four weeks I've thought we've slipped into a bad routine of staying over each other's houses each night and going round quite late and that's taken the spark away. I know this has affected my feelings a bit and it's her first serious relationship so maybe she's overthinking it, I don't know.
She broke contact last night just telling me how she'd got on in a uni assignment and hoping me being away would give me what I need but saying I didn't have to reply. I'm going to respect her wishes and I've been hanging out with friends since this started but I'm worried it's all going to get thrown away.
I asked her when we last met whether she was doing this to break up with me and she said no but she just needed time to miss me and find out what's gone wrong so we can change things. I joked asking if I asked her out in two weeks what would she say and she said it's highly likely she'd say yes. I just need help, I can't see why this has become such a serious doubt and am worried the worst may happen.