You can sync the categories manually and from this article, you will get to know the way to do it. To sync the category follow the below steps.
Login to WooCommerce Backend
Navigate to the Products ▶ Category, You will be redirected to the Product category page. Here you will see the list of categories created.
Here on the category list, Either you can sync each by clicking on the Sync button in the Action column. By clicking on it, immediately respective Categories will be synced in the designer tool.
In order to sync categories in bulk, you have to first select the categories by clicking on the respective checkboxes and click on the Sync all button.
After syncing the categories successfully you will view the sync status will be changed as “synced”.
Note: You need to delete the Categories manually from both sides. If you delete the Category from WooCommerce, you should delete it manually from the designer tool, too.