Missing migration filters that are replaced with filter_null may have invalid settings applied

Small hint if anyone is still having this issue during a Drupal 7 to Drupal 9 Migration:

You can skip the empty filters through migration, by adding the "skip_on_empty" plugin in your "upgrade_d7_filter_format" migration yaml.
Either by directly inserting it in the process pipeline:

process:
  filters:
    -
      plugin: skip_on_empty
      method: row
    -
      plugin: sub_process
      source: filters
      [...]

Or through the usage of hook_migrations_plugins_alter():

  foreach ($migrations as $migrationId => &$migration) {
    if ($migrationId == 'upgrade_d7_filter_format') {
      array_unshift($migration['process']['filters'], [
        'plugin' => 'skip_on_empty',
        'method' => 'row',
      ]);
    }
  }