will i end up with flat beer?

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recapping my bottles? Will it ruin the outcome of my beer?

I was wondering if my beer will end up flat no carbonation because i ended up recapping the whole batch. I recapped the batch after i didnt have enough in the bottles. So i poured more in two days after bottling to top them off so i wouldnt have any explode on me.. The main thing that im worried about is that they will not carbonate now?