Depending on what type of central air circulation system you have will decide how much of the smell/scents/deodorizers move from one room to another via the central air system. The frequency in which you change the air filters to your heating/cooling system will also have an effect on how much of the 'fumes/smell' travel from one room to another, since you keep the door to the chin's room closed. (Also, changing the filters frequently tends to lower your utility cost and causes less strain on your heating/cooling system while making it work more efficiently.) Nothing works 100%. During the spring, summer and fall months, we often are able to open the windows to 'air-out' the house. Air pollution inside most homes is worse than the air pollution outside, especially in the winter months, because the lack of fresh air circulating within the home itself. I usually keep at least two windows (one upstairs and one downstairs) in the house cracked year round. Only 1/4 inch to 1/2 inch can be a huge help in supplying fresh air in your home without changing the temperature or heating/cooling bills drastically.
Keep in mind germs from the flu or a cold (and other sources) not only survive, but thrive, in the normal temperature in most homes. Everyone needs fresh air!
And, yes, chinchillas are capable of having the flu or a cold or anallergic reaction ... but ... their lungs are very tiny and are not developed to withstand exposure to these viruses. When others are sick, do not let them near your chins. If you are sick ... wash your hands, wear a mask and have an apron or cover you can wear over your clothes when you enter their room to care for them. They are much like little babies and you are their parent(s). Protect them.
Keep us posted!
Jo Ann