Each element in the storage.getChanges list has a status: existing and currently used in Redactor files and images are true, and those deleted by the user are false' Now you know which files can be safely deleted from server (hint: those with false status) and you can delete these files using their ids.

Here's an example of storage.getChanges method in use:

var changes = $R('#content', 'storage.getChanges');
for (var key in changes)
    if (changes[key].status === false) // element was deleted
    else // element is still in the content

Here's an example of an object that is returned by getChanges:

"some-id: {
    id: "some-id", // an id of a file. This id had been set during upload.
    node: img, // or 'a' DOM node of element
    status: true, // or false if element is deleted
    type: "image" // or file