I actually haven't tried switching the Rio and Empeg logos with each other on the Mark1 player since the 2.0 software release.

In theory, the Mk1 and Mk2 should behave the same. Select the "I have a Rio" or "I have an Empeg" option in the Logo editor, and then send or delete a custom logo, and it should switch the bootup personality accordingly.

There shouldn't be a problem as far as I know.