There are no mind readers here. Always post the command line used (or log file
line two) so we know what you are talking about.

> the pdf files that already exist on my disk are
> downloaded again. I don't want them to be downloaded

No, they will not.
During an Update, HTT will ask the server has this file changed and will only
download it if it has.

Updateing is fast. I get about 3 files per second. Dependent on the round trip
time to the server. Independent on the size of the files.

Only dynamic html files (which are always new) and moved, updated or restored
files (webmaster changed the date inadvertently) would be redownloaded.