Unfortunately, we do not support the "ignore folder" feature at the moment. I am sorry that the File Administration is causing the problem - we will inspect the scenario you have explained and fix the problem for one of the coming versions.
The only workaround I can think of at this moment is modifying the folder structure so that this folder is not in or under the root of Sitefinity site.
I am sorry that I was not able to help you more. Let us know if there is anything else we can do for you.
the Telerik team
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