Can't uninstall module because of checkbox field
You could create a custom form and set all the field values to NULL in the submit handler. 

For example:

&lt;?php

namespace Drupal\mymodule\Form;

use Drupal;
use Drupal\Core\Form\FormStateInterface;
use Drupal\node\Entity\Node;

class TestForm extends FormBase {

  public function getFormId() {
    return 'test_form';
  }

  public function buildForm(array $form, FormStateInterface $form_state) {
    $form = [
      'test' =&gt; [
        '#type' =&gt; 'submit',
        '#value' =&gt; 'Clear field values',
      ],
    ];

    return $form;
  }

  public function submitForm(array &amp;$form, FormStateInterface $form_state) {
    $query = Drupal::entityQuery('node');
    $query-&gt;condition('type', 'menu_link_content');
    $result = $query-&gt;execute();

    $nodes = Drupal::entityTypeManager()-&gt;getStorage('node')-&gt;loadMultiple($result);

    foreach ($nodes as $node) {
      if ($node instanceof Node) {
        $node-&gt;set('your_field', NULL);
        $node-&gt;save();
      }
    }
  }

}