I believe this issue is related to your database collation. This page should give you more idea about it: http://stackoverflow.com/questions/11702432/mysql-utf8-latin-fails-on-duplicate-key-entry.
To fix it, you need to change the database entries that has the old key manually.
Also, ACF PRO has the feature to omit all diacritical marks by default. Unfortunately, it’s not in the free version.
I hope this makes sense 🙂