As to avoid the current issues regarding the imports, I decided to create a custom and manual world-state using the in-game options. Unfortunately such came to no avail, as it seems my choices regarding Eder still isn't working. I selected that he have his faith restored in Eothas and join the Night Market, and indeed he does have an amulet pertaining to said organization. However, the dialog is treating it as though he fled to Aedyr to find his parents; the ending you'd get if you ignored his quest entirely.
Is there a solution to this issue? Is it just this single line of dialog, or is his quest bugged out? I appreciate any help you can provide.