Lost emails after transferring from storage folder to normal account.

Hi

I have recently changed my computer, and i have export all emails from previous computer to a new computer.

I use this for my work email, hence there are hundreds of different folders for each customer.

After importing the emails into new computer, everything all went onto storage folder instead of my normal sales account inbox.

In the storage folder, each customer's folders were created and all the emails are there.

Here is the problem, I read up somewhere that there is no way i can move the entire folder to normal account, I had to select all emails within one folder, move them to another folder, which i have to create. 

So, i have done all that, with only about 2/3 left to transfer so i thought i would give it a rest. Today when i open Window live mail, EVERY single folder that I have moved to normal account are now back to storage folder..

HELP!! I can't be doing this everyday just to find out there is no way i could actually move them.

Any advice would be great!

Thank you!