I’m sorry you lost your two rabbits.
If the samples come back positive for calici it is of course safest to get rid of the cage. The rabbit calici virus(es),more commonly known as RVHD1 and 2 or RHD are very resistant and can survive a long time in the environment. They cope well with freezing degrees and can survive an hour’s washing in 50 degrees. Direct intense sunlight does degrade them though, and there are chemicals that kill them. There is a non-toxic, bunny safe disinfectant for horse-stables that is much used by rabbit owners, it’s called Virkon S. It’s a powder that you dissolve in water and use after you have thoroughly cleaned the areas where the rabbits have been (it won’t penetrate dirt). You soak the area, then let it air-dry. It has no smell. I used it after my bunny Yohio died of something that could have been the RVHD virus. It was before the RVHD2 vaccine was available here, but after the first outreaks of the disease. I didn’t have his body tested for the virus, it was very complicated and expensive back then.
If you get new rabbits, have them vaccinated right away. They should be vaccinated against myxo and both the RVHDs. If you are in Australia, you can only vaccinate against one type of calici virus (lapinject I think the vaccine is called). They say the vaccines take full effect after 2 weeks.
In Europe the RVHD2 is rapidly becoming more common than the “old” RVHD1. This is because it has a longer, symptom free incubation period – meaning seemingly healthy rabbits are contagious for a rather long time before the disease manifests. The virus can be tracked indoors on shoes, on the paws of other pets, it can come in with fresh forage and even hay. It’s also spread by mosquitos and ticks.
There are Faceook groups that map current outbreaks in the UK, but I don’t know if you are in the UK of course.
Here is info about the viruses by Frances harcourt-Brown, a legendary British rabbit vet:
http://www.harcourt-brown.co.uk/owners/frequently-asked-questions/FAQRHD