I thought you just wanted to save yourself the problem of copying large numbers of files.
The changes files shouldn't be a problem. It's a new feature with Angua, which I haven't investigated. But my impression is that it's used primarily for the history field. You shouldn't have any trouble accessing files without a changes file. I've tested it for my own purposes and found that to be true. If you upload a file to the media directory outside of the DW media manager, it will show up as an 'external edit' in the history.
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Edit:
See
http://www.dokuwiki.org/install:upgrade?s[]=media_meta, item 11