To update this thread on what we pursued internally...the short story is we haven't found anything that would make files disappear while moving a folder. We had four engineers review the code invoked when moving folders, threw fake errors at it to test the error handling, dug for any possible reports of issues with the OS calls we're making, and had two of our quality engineers abuse it moving tens of thousands of files across volumes with every odd case we could think of. If we had found something that would actually makes files disappear, that would be a stop-the-presses kind of event, so we took it very seriously. But we haven't been able to find anything.
Thanks to Fisharefast for answering my many questions, and to those of you chiming in to help.
