Deep litter is common in the broiler (meat chicken) industry.  Generally, growers clean most of the litter (bedding and manure) out of the chicken house in the late summer, once the birds of that growout cycle go to market.  Since most commercial houses have packed dirt floors, a small amount of litter remains as the producers don't want to remove any dirt.  They will then add 2 to 4 inches of bedding for the next batch of birds.  Once marketed the "cake" (hard manure on the top of the litter generally around feeders and drinkers) is removed the remainder is often rototilled to breakup any remaining cake and mix it with the remaining litter and finally top dressed with enough fresh bedding just to cover.  This process will occur 5 to 6 times during the year until late summer again when the process starts all over.

There is some value for immunity for common disease organisms that generally cause little mortality, but If a disease problem occurs, it is best to do a complete clean out, allow the house to remain empty for about a month or so before adding more litter to allow the disease organisms to "die".  Commercial producers rarely if ever use lime as it has little if any benefit. 

I hope this helps

Dear James H.,
I would like to thank you for taking the time to provide a thoughtful and complete answer to my query. We VERY  much appreciate your expertise and your generosity in sharing it with us. I will share this information, verbatim with our local poultry club. There has been much argument and few facts. The Extension Service is wonderful! 

With warm regards,
MaryAnn Hardy