I now have almost the opposite issue on my Mac (OS 10.15.4 Catalina, Toolbox 3.9.0)
When I turn on Hide Menu Icons, the OneDrive icon will completely disappear from both the visible and hidden toolbar.
It will reappear after I quit Hide Menu Icons.
Since OneDrive has the habit of getting stuck, I frequently need to use that icon, which prevents me from using this Toolbox feature.