Installation of Vista over a previous version of Vista

Hello,

I have installed Vista over a previous version of Vista
to repair some problems that I had with my first
installation of Vista. The second Installation,
using the Windows GUI Setup from my first Vista GUI
(like repair/upgrade install), was successfull and the
most drivers, files and already installed applications
are ok and I don't have to install them again. But
now I found two hidden directories in C:

C:\$INPLACE.~TR

and

C:\$WINDOWS.~Q

There are some subfolders and I think that
are old files, like a backup. But I'm not sure
and this folders are not very small (~1400 MB)
and (~400 MB) and I would like to save HD space
and delete this files and folders.

Can I safely delete this directories?
Are these files nessacery to run the
new installtion?

Does anybody know if there are other hidden
files and folders after a recovery/upgrade
install which can be deleted? Thanks