Regarding WA's support. This is from the support front page:
WebAssist also offers free technical support for our products via our Support Forum Monday - Friday from 9am - 5pm PST (except major U.S. holidays)
which is probablly why you haven't gotten an exact answer.
Regarding your problem.......I will let support answer exactly why (if they know) you are getting this error, but I can tell you that I have encountered it also. If your FTP transfer pops up a message box and you are offered the option of skipping this file, do so.....if it is just a notification, then click "OK". When I encountered the problem, the upload was not corrupted.....the only problem was just this annoying message. And I encountered it a number of times during the upload since DW adds the _notes folder. I did some minor investigating and could not figure out why but at the end, the app worked...