I would venture the easier way to accomplish things in this case is to use NTFS permissions on the files to 'hide' them from the users. Had you done your folder structure differently, you could have used the 'Browsable' check box in the QVS settings in the QMC to restrict things, but since you have browsable and non-browsable in the same folder, the only 'easy' solution of which I know is to use NTFS to only allow the service account access to those you want the users not to see and leave those that they should see set to the Local Users etc. such that they will see those... Need further use case details if this is not what you are looking for.
When you use the Documents\User Documents area to change things, those settings are generally stored to the associated .meta files, and those are not editable. If you do things in Documents\Source Documents, those are going to be part of the QVPR file information, which will be pushed to the QVServer using a QVServer distribution, you did not say whether or not you have Publisher license, if so, there may be a way to edit the QVPR file(s) to do this, but things may or may update on the QVS side of things as some settings only push on the initial run of the task and the QDS App Data may need to be cleared and recreated with a full push from the QMS service to populate everything such that the distributions will be updated properly.
This is likely a bit confusing, but this is a fairly complex topic to try to explain in the Community post, but hopefully this helps explain things a little.
Regards,
Brett
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