If you have deleted a file in the File Manager from inside your cPanel all is not lost. Just be sure NOT to click on the PURGE TRASH or the contents will be lost forever.
Using the File Manager, left click on the .trash folder icon. This will let you view the contents of the trash can.
Left click on the icon for the file you wish to restore. This will restore the file for you automatically.
If you left click on the file name, you can select MOVE from the right hand window also.
If the above feature does not work, please check into the r1soft icon located in cPanel, seen here: https://portal.my-tss.com/knowledgebase/265/How-to-restore-files-using-the-R1Soft-cPanel-Plugin.html