Renaming a table will not result in the loss or deletion of a Media file by Database Manager. In fact, renaming a table name is harmless, as the Database Manager will uses the table's filename for media files.
Changing the table's filename will prompt by default a message dialog if you want to rename the associated media files accordingly to the new name. If you do not receive this message, it means you have opted out of this dialog, and you have two choices: to rename or not to rename.
Should the Database Manager delete a table (by pressing the delete button, or by adding a new video), it will move the deleted media to the Windows Recycle Bin.