> Is there any way to save the updated files to a 
> different folder from session to session so we can 
> have identified which files are new? If there is no 

Well, this is not built- in, but, using the library, 
this shouldn't be very complicated:

..
  htswrap_add("transfer-status",htsshow_xfrstatus);
  returncode=hts_main(argc,argv);
..

int htsshow_xfrstatus(lien_back* back) {
  /* 200 'OK' status */
  if (back->r.statuscode==200) {
    /* modified! */
    if (!back->r.notmodified)) {
      printf("link updated: %s%s -> %s\r\n",back-
>url_adr,back->url_fil,back->url_sav);

    }
  }
  return 1;
}

> something like 'store the updated files to folder 
> <name of the mirror>.<date of updating>' so the 

This might also be possible, using verbose debug, and 
a specific shell script

You can also estimate the md5 of the file stored in 
back->url_sav filename to ensure that the file was 
new, because some servers always retransfer data, even 
if it was fresh.