> missed.I choose the option "Update existing
> download" and all previously download files
> have been deleted.
The default is to delete files no longer in the mirror.
Your update had problems (see log file) so the mirror was empty (mostly) and
the files were deleted.

1) Always post the command line used (log file line two)
2) I always run with timeout=60 retry=9 so transient problems will not be a
problem.
3) Update again.
4) As for why some links were not captured, you'd need to state the page URL
and the link URL at a minimum..