I didn't use the HxC for this purpose neither.
But I think the HxC should be capable of hosting this kind of special disk images as well - the HxC is agnostic to the content of the disk image, it "only" emulates the physical characteristics of the Emax floppy disk. The special disks for upgrading the Emax have the same physical layout as normal sound bank floppy disks, so it *should* be possible to use the HxC...
... but you said you tried this already and it didn't work ?
How did you make the .HFE with the HxC software ?
As far as I understand the correct procedure would be:
1. Press the "Load Raw Image" button
2. Select "Emax 3.5 DD Floppy disk" in the "Predefined Disk Layout" drop down list
3. Still in the "Raw file format configuration" window, press the "Load RAW file" button and select the EmaxSEUpgrad.img file (the one from the files section with the 800kb size)
4. In the main window, press the "Export" button
5. Save the file as a .HFE file
Is this the way you did it ?
If it doesn't work, the only (and recommended) possibility will be to replace the floppy drive temporarily by a floppy drive, as Ted suggests. But then you'll need to write the image to a real floppy disk on a PC first (using an internal floppy drive and OmniFlop) - I admit this is a procedure which is not that obvious because most people don't have this kind of PC anymore...
Good luck !