I've tried an update with HTTrack Website Copier 3.30-alpha-
06+swf
I don't really understand what you mean in the js.readme 
file by "you have to set an upper recurse level" and "has 
not been scanned " (is at all, even for images and plain 
links?)  but Httrack left the js file untouched and the 
pages calling the js file functions work now as the pages 
linked by javascript are downloaded by a site map (or could 
have been downloaded with scan rules).
Because of a redirection on error 404, it modified the path 
in the other js files of the site and I had to rewrite them 
(I only test in a well known situation ...).

This WinHTTrack update also did a better job on another 
tricky site : I didn't find zero length files.
Still many problems with javascript, but not with Httrack 
modifications.

Regards
Dan