Hi Julia, welcome to the community!
You can read more about the migration/integration between Trello and Atlassian account on the link below:
https://help.trello.com/article/1197-using-trello-with-an-atlassian-account
I don't remember people losing boards and things like that, but if you're having this sort of issue, I would recommend opening a support request at http://www.trello.com/contact
I hope that helps.
Cheers,
Melo
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