Hi Brian,
The XML import method only works to upload and populate new content -- you can't use it to add to already-existing content, unfortunately. If you were to upload the exact same XML files a second time, but with PDF galleys, you would have duplicated issue content in your Archives list, but with one issue in particular having the galley files. This issue has been partially addressed (but not resolved) in Bug 3914:
http://pkp.sfu.ca/bugzilla/show_bug.cgi?id=3914. I'll add a comment to that report to address your situation here.
Cheers,
James