Change the save template in the driver. The default is something like:
Code:
{author_sort}/{title} - {authors}
And that means when you send to device, it will replace the current book with the other book. You can change the template to include something to make it unique. Including the language would work, or the calibre id would make the file unique. So, either of these:
Code:
{author_sort}/{title} - {authors}{id}
{author_sort}/{title} - {authors}{languages}
The languages can be multiples, so you might need to handle that.
When you connect the device again, calibre should match the books correctly. As Kovid said, the metadata.calibre file should have enough to make sure the books match the correct edition. But, that might not be the case for Kobo devices. It might match both editions to the same editions. The first time they match after being sent to the device, can break the linking that calibre originally creates. If that happens, you will need to use the match function in the device list.