I stumbled uppon the same problem as described in this question. In addition, i didn't want to loose the __migrationHistory table from the database.
I tried it with the suggested Solution of using one "super" context which contains all DbSet<>s and using the normal Contexts, but i got a error. ("Model backing DbContext has been changed") This is easily avoidable if you just kill the __migrationHistory table from the SQL server, but as i said, i want to keep the history.
I found a simple and easy solution, see my answer below.