I'm very sorry to hear of your loss.
It is not uncommon for chinchillas to die one after the other even if the problem is not contagious when they are closely bonded.
It is safer to treat it like it is contagious though and think through possible causes. When multiple animals die it is usually pneumonia, mold contamination, or overheating but if they were both old (around 10 years) natural causes cannot be ruled out.
A big one to consider is mold contamination of the pellets or hay. Always smell hay before you buy it. I have a lot of problems here in Georgia. Chinchillas' diet should be restricted to hay and pellets as many things can be poisonous to them. Most chinchilla owners give treats but the kind of treats they can have is extremely limited. Environmental temperature should never exceed 75F, although 73F is a safer upper limit. Pneumonia, unfortunately, is sometimes spontaneous, but I think it is most often caused when a chinchilla looses weight for other reasons (especially upper respiratory infection), and then becomes more vulnerable to it. Almost always pneumonia is fatal in chins.
For future reference I recommend to all pet owners to weigh your chinchillas once a week and keep logs. A steep decrease of 15-20% of healthy weight indicates illness and requires prompt diagnosis and treatment. The trend itself can also be helpful in diagnosis. Always keep track of daily food and water consumption and fecal output. It's harder to do with two in a cage but not impossible. With my chin I measure his water with a ruler fastened to the bottle but you don't have to go to that extreme. I caught a clog in the watering system and an abnormal reaction to antibiotics using this method so it is very effective.
I recommend using bleach because vinegar is just not a very strong disinfectant. It leaves no harmful residue and kills pretty much everything. The downside is that bleach fumes are highly toxic until the solution dries and should not be used around chins, birds, or any small animals in the same room. The plastic pans should be bleached as well. Clean them last to avoid cross-contamination. If the plastic shows signs of being chewed replace them with metal pans if possible. Plastic that is ingested can also kill chinchillas in various ways. Let everything dry in direct sunlight if possible as sunlight also helps disinfect but don't let any birds or squirrels get onto the cage.
The cage can be painted with spray paint marketed as non-toxic after it dries, designed for metal applications. This is common practice with chinchilla breeders. You'll want to clean the rust with a cleaner such as CLR first. Make sure it is rinsed well afterwards an thoroughly dry before painting. Your cage should be as good as new.
Be sure to install wooden shelves in the cage as well. They are important for your chinchillas' well being.
