Followup ...
First, thanks for reporting the problem.
The problem was more basic than the scenario you found. As far as I can tell, any time a book was sent because of "sync books" the cover thumbnail was removed. It is replaced in a later connection step. Unfortunately, if the connection is interrupted after a book is "synced" but before the connection stabilizes then the cover thumb is lost until the metadata for the book (last modified) is changed.
The fix is in calibre and will be in the next release.