A key concern is very small particles created when fogging being carried throughout the building and inhaled. Disinfectants in someone's lungs is not a good thing. Additionally, fogging is not really effective for some of the things people try to use fogging for.
If done with proper precautions fogging with a sanitizer in ducts can be done following cleaning.
For odor control, I would prefer use of Vaportek for ducts.
YES. You MUST at times encapsulate duct work after cleaning for some situations including; heavy smokers, fire, sever pet contamination, heavy candle burners or heavy curry oil contamination to name a few situations.
You do use a fogger in some situations to apply product like an encapsulate. Unsoot makes a great product for these applications.
First the home must be empty of All people and pets, including snakes, hamsters etc. Make sure you are wearing an appropriate respirator for the product you are applying.
YOU MUST BE USING NEGATIVE AIR MACHINE for your cleaning process. If you are using a TM or other method you will NOT get good coverage as a fogger will only project so far.
Once you have cleaned the system, hook your 10 inch line up and cover all the vents as you normally would for cleaning. One by one go to each opening and fog each opening while the negative air machine is still running. This will draw the encapsulate all the way down through the vent line back to the main line where your negative air machine is attached. This is the ONLY way to get good product coverage which is necessary with smoke, odors and curry oil in order to seal it in completely. It is also necessary as it limits the amount of product that does go ai born into a house. If you are using gas powered and or truckmounted negative air equipment It allows you to fog in a home that folks are living in without contaminating there furniture and belongings. Because MOST excess product gets sucked outside and through your equipment.
AS for fogging other products into HVAC systems, there are options out there that are EPA approved for duct work application. A very affordable one that is good for general duct work sanitation is called Envirocon. Again the application is done in the same way as I described above with the same precautions. Follow the instructions on the product you are using and you will be fine.
Hope this helps some.
PS...............There is good money in encapsulation duct work. We charge $20 to $30 dollars per vent or return in homes to encapsulate. So a home with 15 vents and 6 returns would add $630 dollars to the cleaning bill as cleaning is required before any encapsulation or treatments can be applied. Encapsulate does NOT stick to dirt and debris very good. Takes 2 guys an extra hour on a job to apply it and $50-60 dollars in product on that size job to get good coverage.