Problem regarding two accounts i had on my square enix account.

First of all i played open beta on my Final Fantasy XIV 1, once i got my early access code and went registering it, i noticed the Final Fantasy XIV 2 had my bought Digital Copy and 1.0 CE Onion helm, which was strange it had two of my bought games.

Did i loose all my progress from open beta now, and do i need to play from fresh again since the Final Fantasy XIV 2 don't have the characters i played open beta on.
I wish there was info to know that my digital copy went on the XIV 2 account, not XIV 1. And Final Fantasy XIV 1 account shows only that it was registered to beta.

I ended up with 2 accounts as you stated as well from the beta of 1.0. I made sure to warn my friends about it too because when I went to apply my pre-order to my account it defaulted to my first account I made Final Fantasy XIV 1 which has been cancelled for a long long time. My 1.0 CE was applied to Final Fantasy XIV 2 where the onion helm and all those items are. That is the current active account and where you will want to apply the pre-order code unless you want to have another account with another subscription.

If you applied your pre-order code to Final Fantasy XIV 1 you likely lost the CE 1.0 stuff since it is attached to the other account. Maybe SE can help you out with that. I would think they could correct that for you. Since your problem is pre-order related and I would not blame you for wanting to keep progress on the same account I would call them, email might take too long. But yes, I came very close to making the same mistake.