I'm not quite sure, starscream.
Most of the time, these files are "zero-byte" files and they contain no data (at least, none that I could see). They're some sort of residue that is left behind after a failed or an incomplete upload.
In the same vein, Pure-FTPd per se is simply a free BSD FTP server. That explains the file(s) naming convention. I suspect that the reason these files are difficult to delete is because they include too many "dots" in them. I can't be sure about this, though, since it's been years since I last used a Linux or a BSD, and I can't remember how many dots Unix-systems allow in file names.
So, to answer your question, I don't think these are log files, for the simple reason that they don't seem to contain any log data. However, I might be wrong.
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