I have read the first five Dune novels and after the first I do not recall any further mention of Imperial conditioning. In the novels written since Frank Herbert's death, were any further references or details given about what this process actually involved and why it was considered virtually impossible to remove?
Well, it's suggested that it's some form of Psychological Conditioning. I can't find any clear indication of how it's done, but that seems likely from the term, and none of the references I've found in the books I have seem to counter it.
Also, given that it is broken via psychological means, that would pretty strongly suggest it's a mental conditioning.
Now, since you asked about references, here's what some quick searching found:
“Hawat will have divined that we have an agent planted on him,” Piter said. “The obvious suspect is Dr. Yueh, who is indeed our agent. But Hawat has investigated and found that our doctor is a Suk School graduate with Imperial Conditioning—supposedly safe enough to minister even to the Emperor. Great store is set on Imperial Conditioning. It’s assumed that ultimate conditioning cannot be removed without killing the subject. However, as someone once observed, given the right lever you can move a planet. We found the lever that moved the doctor.”
“How?” Feyd-Rautha asked. He found this a fascinating subject. Everyone knew you couldn’t subvert Imperial Conditioning!
Then Jessica and Thufir talking about it:
“Is there a traitor among us?” she asked. “I’ve studied our people with great care. Who could it be? Not Gurney. Certainly not Duncan. Their lieutenants are not strategically enough placed to consider. It’s not you, Thufir. It cannot be Paul. I know it’s not me. Dr. Yueh, then? Shall I call him in and put him to the test?”
“You know that’s an empty gesture,” Hawat said. “He’s conditioned by the High College. That I know for certain.”
Later, it being psychological is backed up by how they broke it:
The Baron nodded. “Oh, yes. Now, I remember. So I did. That was my promise. That was how we bent the Imperial Conditioning. You couldn’t endure seeing your Bene Gesserit witch grovel in Piter’s pain amplifiers.
Then, from the Appendix to Dune:
IMPERIAL CONDITIONING: a development of the Suk Medical Schools: the highest conditioning against taking human life. Initiates are marked by a diamond tattoo on the forehead and are permitted to wear their hair long and bound by a silver Suk ring.
PYRETIC CONSCIENCE: so-called “conscience of fire”; that inhibitory level touched by Imperial conditioning. (See Imperial conditioning.)
Then, from Children of Dune:
Suk doctors? Their conditioning supposedly guaranteed them against disloyalty to their owner-patients. Suk doctors came very expensive. Increased purchase of Suks would involve substantial exchanges of funds.
Now, going to the newer books:
From House Harkonnen
“You, sir, are a Mentat, accustomed to selling your thoughts and intelligence to any patron.” Yueh drew his lips together and studied de Vries as if he were performing an autopsy . . . or wanted to. “I, on the other hand, am a member of the Suk Inner Circle, graduate of full Imperial Conditioning.” He tapped the diamond tattoo on his wrinkled forehead. “I cannot be bought, sold, or rented out. You have no hold over me. Now, please allow me to return to my important work.”
In Sandworms of Dune:
(I've omitted some irrelevant references, like him talking about drawing the tattoo back on his forehead.)
In his first life, he had broken his Suk conditioning. He had failed his wife Wanna by allowing the Harkonnens to use her as a pawn and had betrayed Duke Leto, bringing about the Atreides downfall on Arrakis.
Yueh touched his own smooth, unmarked forehead. "We're starting over, Jessica. Blank slates. Look at me. The first Yueh broke his Suk conditioning - but I was born without the diamond tattoo. Entirely unblemished.
The evil Harkonnens had known that Wanna would be the key to breaking his Suk conditioning, and it had only worked - could only have worked - because Yueh loved her with all his heart.
Unable to break his conditioning, Yueh shuddered and spasmed. He wanted nothing more than to do as the Baron demanded. "I... can't!"
The memories were so clear to him that his entire body felt like a raw wound: Wanna in agony and the sharp, broken-crystal pain of how his Suk conditioning had been thwarted.
In his restored memories, he saw with clarity when he had become an actual Suk doctor, when he passed through an entire Inner School regimen of Imperial Conditioning and took the formal oath. " 'A Suk shall not take human life.'"
From Dune: House Atreides
After years of training and conditioning, all Suk doctors seemed compelled to take themselves far too seriously.
As heir to the Golden Lion Throne, Shaddam was familiar with Suk Imperial Conditioning, which guaranteed absolute loyalty to a patient. In centuries of medical history, no one had ever managed to subvert a graduate of the Inner School.
There may be more, but that's all I could find in a quick search.
It is my understanding that this will eventually be explained in an upcoming book. Recently published, Sisterhood of Dune is the first in the "Great Schools of Dune" series and explains some of the back-story of the Bene Gesserit sisterhood.
Frank Herbert left filing cabinets and boxes of notes devoted to the back-story of the Dune universe, and his son Brian is publishing much of the material.
The second book of the series, Dune Messiah, contains the following passage. This is from the scene where Edric of the Spacing Guild presents Emperor Mua'dib with the Duncan Idaho ghola:
The Tleilaxu displayed a disturbing lack of inhibitions in what they created. Unbridled curiosity might guide their actions. They boasted they could make anything from the proper human raw material -- devils or saints. They sold killer-mentats. They'd produced a killer medic, overcoming the Suk inhibitions against the taking of human life to do it.
So, although the actual process remains a mystery, it's apparently a guard - either a biological one or psychological - against the taking of human life.