Overview
You are experiencing an issue where deleted documents are not automatically removed from the Favorite Documents Web Part.
Solution
This issue was isolated to earlier releases of the Bonzai Favorite Documents Web Part. The issue is resolved in Bonzai release 2.2.12 or later.
You can upgrade to the latest Bonzai version by viewing the latest Release Notes. The steps for upgrading from version 2.1 to version 2.2.X can be found in How to Upgrade to Bonzai Version 2.2.X.