Set default for 'Update Fields' to Yes, and add the option to store the choice.

src/Plugin/WebformHandler/FormProcessorWebformHandler.php

@@ -163,7 +163,7 @@ class FormProcessorWebformHandler extends WebformHandlerBase {
           $form['additional']['fields']['update_fields'] = [
             '#type' => 'select',
             '#title' => 'Update fields (this might delete the fields from your form)',
-            '#default_value' => 0,
+            '#default_value' => $this->configuration['form_processor_update_fields'] ?? 1,
             '#options' => ['0' => $this->t("No"), '1' => $this->t("Yes")],
           ];
           $form['additional']['fields']['help'] = [
@@ -283,7 +283,7 @@ class FormProcessorWebformHandler extends WebformHandlerBase {
       $builder->deleteFields($values['additional']['fields']['field']);
       $builder->save();
     }
-    unset($this->configuration['update_fields']);
+    $this->configuration['form_processor_update_fields'] = $values['additional']['fields']['update_fields'];
   }
 
   private function getContactId() {