Do you have CCleaner? Is it set to under Tools > Drive Wipe to Wipe Free Space on that drive? Then uncheck that, delete the folders. By free space, CCleaner means space occupied by already deleted files [the files often still exist unless overwritten, but the pointer in the file manager is altered so as to show them as deleted].
If it is not set to wipe free space then it is playing at wiping some drive space, so uninstall CCLeaner, reinstall it, and delete those folders.