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After an Organization Logo is uploaded and added to ArcGIS Online, there is no option to remove the logo. The uploaded logo can only be replaced with another new logo by configuring general website settings.
This is a known limit.
Instructions provided below enable the user to replace an existing Organization Logo with a transparent image (PNG) file. This nullifies the logo and displays the Organization name only.
It may be necessary to left-click and drag the pointer to highlight the region of the blank logo. This guarantees the logo has loaded on the browser correctly.