You should not be manually writing or changing any files in the Clarity filestore location, instead you should have a separate staging location/folder on the server where the bg service is running and for the document to be consumed from there instead, and it will then create the file appropriately (with a different name and folder structure) in the filestore when it succeeds.
Take a look at the sample files in the XOG client /xml folder which provide some examples that show this:
C:\ProjectX\xog\xml>findstr /i /n /c:"parent doc" *
change_write.xml:15: <Parent documentLocation="/niku/xog/test/documentXogLocation/change">
documents_write.xml:5: <Parent documentLocation="E:\niku\8.1\build/xog/test/documentXogLocation" parentObjectId="1010" parentObjectType="KS">
C:\ProjectX\xog\xml>
The location and files chosen should have no permission issues for the user running the bg service to read from either.