For future readers: Stephen and I were able to work this out over email. Mainly, the key is to ensure that your emote version matches your H9000 version. If you have an H9000R, you must update your H9000R through Emote before updating Emote itself.
Another thing to note is that your Emote version number can be found by hovering your mouse cursor over the Eventide logo in the bottom right hand corner of Emote. The version number next to "Software Version" in the H9000 info panel is not your Emote version, but your H9000 version.
Thanks Stephen for helping to work through this!