I don't know about deleting files for things already installed, but I do not not believe Command Center has any way to detect things being in place, if it didn't do the installations.
I went into the settings (top right of the Command Center UI), and I changed the download path to be on a different larger drive than its default of the C: drive. I have a Solid-State drive for my C: drive, so I try to keep all downloads and anything other than Windows and applications on it.
Bob Bone