If you deleted the file but forgot to use the SVN command, right-click the folder containing the file and select Check Changes. In the dialog box that appears, the deleted file will be displayed with the status as "missing." There, you can right-click it and select “Uninstall” for Subversion to understand what you want. If you do not want this to disappear, you can right-click it and select "return".
If you renamed, moved or copied it, it is best to rename / move it or delete the copy, and then use the appropriate Tortoise command correctly. Otherwise, you will lose the history link between the old file and the new file.