I had an issue where after upload the HTML of some pages would be corrupted, such as the last couple of lines of the old page appearing after the final </html> of the new upload. Only intermittent, actually a bit uncommon, but very annoying when it happened. I was publishing via an external FTP client, and one day (after it had happened a couple of times in one day) I dumped the client I was using and switched to another. Hasn't happened since.
The other workaround is, of course, to delete the old stuff before uploading the new, but being free to avoid that step is nice.
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