I woulda sworn I'd done it that way in the past, but, hey, I've been wrong before.
It is indeed possible that you have managed to achieve this before without the unit throwing an absolute fit about it. Fairly unlikely, but possible.
But, anyway, yeah. Now you know for future reference, the intended flow is replacing the files in /.rockbox with those of the shipped update .zip file, in their entirety.
The best, or certainly the easiest, way of achieving this is to simply open the update .zip with your archive manager of preference and then select extract with the root of the DAP as the endpoint. Some archive managers will offer a right click context menu shortcut for 'Extract to ...' which would also allow you to select the root of the DAP as the endpoint.
When prompted as to whether or not you wish to overwrite the existing files on the volume select 'yes to all', and then 'done', and eject the volume from the host.
Rockbox should now detect that it has been updated and prompt you to reboot the device, at which point the update will be complete.