If you have bought some books from Kobo, you can ask them to move the books to the new account. They did this for me when I had a wierd problem a long time ago.
And to help prevent it happening again, you can turn collection syncing off. In the config file, add the following line in the "ApplicationPreferences" section:
If you are doing this on a Windows machine, make sure you use a Linux line-ending aware editor. I recommend Notepad++.