Feature revert deletes existing Strongarm variable
In case someone gets on this question: We finally managed to find the answer to our problem.

We had an old version of the strongarm module (7.x-2.0-beta2) instead if 7.x-2.0 which is stable now (since 2012). The update hook from this update saved a lot of variables from the features to the drupal variable table, and on every further feature revert, no more variables would be deleted, so the problem was fixed. Credits to @Weri!