I gave the GL data backup file to our auditors to import the trial balance into Caseware. They were able to import the TB but for accounts with both an account and department number, the account code became the department and the department code became the account. Do you know why this happened?

Because they had the wrong options set for the Caseware retrieve?

Caseware does have an option to "Invert acct. numbers" for some interfaces. Perhaps this applies to Adagio. This really is a question for Caseware.