It sounds like you have a text file containing a list of links. Use the --list
option to make HTTrack download all the links in the file.

HTTrack will overwrite anything that gets in its way when it is downloading.

To avoid losing the files you have, make a backup of them, and start HHTrack
in a different folder.

To avoid waiting to download them again, remove them from the list before you
start HTTrack.

If you don't want to do that, you could tell HTTrack to ignore them using a
negative filter. <http://www.httrack.com/html/filters.html>

HTTrack copies your list to a cache and uses that when you start it again.
HTTrack ignores the original list after you create a project, so removing them
from the list will have no effect.

By default when you resume HTTrack it checks for updates to existing files
before downloading other ones.

If you want to skip the update check, try using the --cache=1 option. This
should make HTTrack start downloading new files immediately.