The layout of HTTs directories is
BasePath 
--- index.html 
--- projectName1 
---/--- index.html 
---/--- hts_cache/new.txt
---/--- web/index.html
---/--- web/jpg/background.jpg
--- projectName2
---/--- ...
...

BasePath\ (See <http://www.httrack.com/html/step1.html>) All mirrors are in that
directory.
BasePath\index.html points to all the projects so you can select which one to
display. If there is only one project, it automatically forwards to that.
BasePath\ProjectName1 contains all files related to that project where
ProjectName1 is what you called the first project.
BasePath\ProjectName1\index.html points to all the urls in the URL box (See
<http://www.httrack.com/html/step2.html>) If there is only one URL it auto
forwards to that.
BasePath\ProjectName1\hts-cache HTT use
BasePath\ProjectName1\web This is where the site files are. web depends on
your local structure.
BasePath\ProjectName1\web\index.html
BasePath\ProjectName1\web\index1.html
BasePath\ProjectName1\web\jpg\background.jpg
...
BasePath\ProjectName2 next project if any.

You copyied the BasePath... directory structure to the new site.
Instead copy the projectName1... directory structure to the new site.