The Joomla! permissions are very comprehensive but for the first few times they are often confusing. The basic use of the Permission Reset tools is to get back to a known state.  The tools simply go through all the Downloads and all the jDownloads Categories and set the permissions to Inherited.

Usually it is helpful to also 'reset' the Component level Download Permission. of every User Group to Inerited as well.  One can access the Component Permissions from the Options button on the jD Control Panel page.  After doing that then no one except Super Users can Download.  So it is now a safe state.

Basically that is all there is to it.  However the following notes give some examples of what happens.

This article uses the Public user group of a category as an example.  Treatment of Downloads is the same as for Categories. The reset process searches the entire set of categories or downloads as appropriate.

The default status for the Public Group of the selected in this example is as shown opposite.  The permissions were ultimately derived from the Public permissions set in the Component permissions.
And the picture opposite shows the default permissions for the Registered Group of this category.
Now let us change the Public group permisions of the category to the situation opposite.
There is an effect on the Registered group permissions as the Public Group is the Parent of the Registered group.
Now suppose we use the  tool. After a short delay the Public Group permission become as shown opposite, that is they have all been reset to Inherited. A message such as will be shown.  In this example we only had one category with a user group download permission set to 'Allowed' or 'Denied'.
The effect on the Registered group is as shown opposite.
Now repeat this but this time do not set the Download permission to Allowed or Denied. This time the message is displayed.
In this case because the Download permission was left at 'Inherited' no changes were made to the permissions for the Public group of the Category.

Colin Mercer January 2015