This is an issue our team is currently investigating.
The linking process automatically generates a BNEA account for you based on the e-mail you previously used to play Duelyst. If you created an account independently of this process, the system may now have locked you out from properly linking accounts.
Our current suggestion would be to use alternative Duelyst clients and try logging in with your BNEA account:
Using different clients has helped other users progress past this issue.