Deleting shortcuts to files won't delete the files or folders. Need a bit more details here. You have a phone connected to a PC, you see the file list for the storage on the PC, you deleted the files. Does the storage show less files in uses? What you mean it's showing the memory? If the card has any files on it, it will show up.
What was the free space before you deleted what you deleted? And exactly what files did you delete? Folders, files, shortcuts? From where did you delete them?