1) Always post the ACTUAL command line used (or log file line two) so we know
what the site is, what ALL your settings are, etc.
2) Always post the URLs you're not getting and from what URL it is
referenced.
3) Always post anything USEFUL from the log file.
4) If you want everything use the near flag (get non-html files related) not
filters.
5) I always run with A) No External Pages so I know where the mirror ends.
With B) browser ID=msie 6 pulldown as some sites don't like a HTT one. With C)
Attempt to detect all links (for JS/CSS.) With D) Timeout=60, retry=9 to avoid
temporary network interruptions from deleting files.

> I found that after 49,000+ files were downloaded
> (all pdf files) I had to stop the program and redo
> some of the settings. When I started the mirroring
> again I found that httrack deleted 18hrs+ of work

Did you click Cancel just once and wait for it to finish?
HTT purges files (unless you check Do Not Purge) at the END of a run so the
mirror matches the site.

> is going to delete all my work before continuing. 
At the END of a run not before continuing.