> I don't think it would check the entire contents of
> a file, but rather just compare the filesize and
> date-last-modified HTML header of existing files,
> and will also add new files.

Yes, and the fact that all files are modified is 
totally normal: the engine always rescans the complete 
structure (using the cache generally, or using the 
cache AND remote timestamps), to match potentially 
modified options. But this doesn't necessary mean that 
you'll redownload data ;).