You can move the file every time, but we'd hoped by now that everyone would be using the latest bootloader, as it's been available for a considerable amount of time and changed the behaviour to look in the .rockbox folder first, then outside it if the file wasn't present.
If you re-install the bootloader (take an original iriver firmware, fwpatcher it with the newest version, boot into the iRiver firmware, and choose to do a firmware update) the newest one will handle finding it in /.rockbox/