Overwriting Files & Deleting

I have redone an existing web site done by someone else (originally in FrontPage) into WebStudio. I have uploaded all of the new files, but the old FrontPage files (which I am not familiar w/) are still what the server is pulling.

The folders/subfolders look like this ...
.filter
.gnupg
.svn
.propbase
.props
.txt-base
.tmp
.panel
.svn
.cgi-bin
.date
.recycle-bin
.users
.web
.vmailmgr

If I delete these files will I hurt anything? or will it just take out what I need for the new uploaded files to become effective?

There is also a phpBB message board like this one attached to the original website/host which i don't want to screw up by deleting the wrong files.

Anybody?