> The 1st mirror is 000406 followed by 000405 and then 
000403.
> However, the 'hts-cache' subdir of 000403 and 000405 are 
emtpy.

Probably a directory directive problem -- even if the 
mirror was empty, httrack ALWAYS create at least doit.log 
and new.dat/ndx/lst files. I suspect that the cache of the 
first directory was changed, isn't it? 
By the way, are you using the commandline httrack? Ensure 
that you use the -O option correctly, and if necessary, 
delete the previous hts-cache/doit.log (it will be read for 
updates, which could cause problems if the -O option is 
there)

Therefore, you have two ways of updating a mirror:

httrack -O foo www.foobar.com -c4 ..more options
and then, to update,
httrack -O foo --update

(all options and URLs will be read in the hts-
cache/doit.log file)

The cleaner and preffered version for "production" mirrors 
is:

httrack -O foo www.foobar.com -c4 ..more options
and then, to update,
del foo/hts-cache/doit.log
httrack --update -O foo www.foobar.com -c4 ..more options

So that you can be sure that no "garbage" options are read 
in the previous doit.log file (normally, when specifying 
URLs during an update, httrack automatically bypass this 
file, but it is safer to delete it, and it is the way 
winhttrack and webhttrack are using)

> I'm also confused by another thing: Should I use both a 
new
> Base Path and new Project Name for each new mirror or 
should
> I just change the Project Name alone?
Just change the project name, the base path should never 
change.