Hello @azadbakhsh,

Thanks for reaching out to us.
When checking the same scenario on our test environment, it was found to be working fine. We tried to add, remove and overwrite options with existing categories, and the breadcrumbs changed as per the updates. Could you please try clearing the cache once the filtered products are updated? Also, kindly confirm that you are using the latest version of the plugin. If you can share a video reference that would be great as we can see the way that you updated categories.
Also please do a plugin compatibility test and let us know the feedback.

Looking forward to hearing from you.