I'm sorry for your loss. That must have been so hard to let your bun go.
Friskiee2, Rhd is not the same as EC. Rhd is a hemorrhagic viral disease, EC is a parasitic disease.
Rhd is actually a more sudden illness and is quickly fatal. I wouldn't have suspected rhd without there being other symptoms of the disease present(bleeding, convulsions, complete flaccid paralysis and lethargy), but I guess is possible. Usually with floppy rabbit syndrome, the flaccid paralysis involves the front limbs as well, while the rabbit remains alert and willing to eat. With EC the onset isn't usually so sudden. So sudden paralysis is not as likely to be caused by EC.
http://www.bio.miami.edu/hare/paresis.html
http://wildpro.twycrosszoo.org/S/00dis/Miscellaneous/Floppy_Rabbit_Syndrome.htm
http://wildpro.twycrosszoo.org/S/00dis/Parasitic/Encephalitozoonosis.htm
If it was rhd that was the cause of death, then your other rabbit is very much in danger of contracting the illness as well because of how contagious it is even though they were separated. The disease can be transferred by you handling one rabbit than the other. If your other rabbit doesn't end up sick then it's highly unlikely that rhd was the cause of death for your first rabbit.
https://www.harcourt-brown.co.uk/articles/infectious-disease/rabbit-haemorrhagic-disease
https://rabbitwelfare.co.uk/rabbit-health/rabbit-vhd/
If your rabbit continues to be alright and is not currently vaccinated for rhd1/myxo and rhd2(two separate vaccinations), then I would suggest talking to a rabbit savvy vet about having that done right away.