> What is needed to merge 2 downloads manually, can I 
> generate the new.txt new.zip from my harddisk ?
This is not an easy thing to do - basically you need to 
merge the two ZIP in one. You could uncompress the two, and 
recomopress all files .. but filenames are generally 
incompatible with filesystem naming (filenames are actually 
URLs, including query string) AND httrack needs meta-data 
stored in the ZIP file (containing HTTP headers), so this 
isn't an easy thing to do.

> Are both file needed ?
Yes. The txt file is the "local" catalog, allowing to purge 
remotely deleted files.

> Is there an option similar to wget --noclobber
> or time stamping option: 
>  --don't re-retrieve files unless newer than local.

HTTrack always uses etag+date to limit download. But there 
is not yet any option to avoid clobbering files already 
downloaded (that is, if the server did send the file anyway)