Expected: Upon manual cache refresh W3TC will attempt to push files to CDN, if identical files exist, will not attempt to transfer a 2nd time (and will not result in error), and minified files will be properly served by CDN via rewrite rules.
Actual: Upon manual cache refresh W3TC attempts to push files to CDN, if identical files exist, the transfer results in an error (and is placed int he queue) and files are served locally (although manual replacing the local domain with the CDN domain properly serves the files).
Temporary Fix: Enable Force overwrite (but this is not desirable for production as it overwrites files that need not be overwritten thus making unnecessary calls.), or modify the CSS/JS files, thus forcing a transfer to the CDN.
Perhaps either A: force overwrite on manual refresh, or B: prevent the transfer from erring out and ending up in the queue if an identical file already exists. I cannot confirm that this problem persists with the regularly transfer modified files option, but can confirm that enabling the option does not resolve the problem.
(Preview mode is disabled in my case, and the transfer queue has been emptied.)