Sub-theme preprocess inheritance
Subtheme inheritance is a bit different in D8. I believe you are running into expected Drupal 8 Theming behaviour.

In D7, the parent theme's functions were called, followed by the subtheme's preprocess functions - I hope this is still the case, but it seems from your troubles that it might not be.

When in doubt, just duplicate the corresponding file in your subtheme.

Here's some more reading on the subject:


https://www.drupal.org/docs/8/theming-drupal-8/creating-a-drupal-8-sub-theme-or-sub-theme-of-sub-theme
https://www.drupal.org/docs/8/theming/sub-theme-inheritance