The immunity was because a bureaucrat could not be expected to know about the 3rd amendment. Any future violation would be a decision made by a bureaucrat, the same immunity would apply, and the precedent would say that the state wins.
For all intents at this point, the 3rd amendment is null and void.
Qualified immunity gives immunity to many government actors who violate Constitutional rights unintentionally, because the law is not clear at the time. Getting qualified immunity on remand is basically a one-time victory. If you win on qualified immunity because the rights are not clear, but at the same time hold that there are such rights, then that gives fair notice to government actors and they don't get to do it again.
The idea is that you don't want to make the government too cautious because they might get sued if they arguably violate someone's rights so you give them the benefit of the doubt, until the law is clear enough and there is no more doubt.
There was a recent case of a woman who was tazed in Seattle for refusing to sign a parking ticket. She lost on QI grounds, but they also held that it was excessive force. That basically establishes that if the police do it again, the next person can successfully sue. That doesn't mean the police are free to taze people for refusing to sign traffic tickets. It just means that the court says "this is your only warning" and lets that case go at that.
This is different from absolute immunity, which means for example, you can never sue a prosecutor for unfair prosecution tactics used in the courtroom, and you can never sue a judge for ruling unfairly.
The standard for qualified immunity is that bureaucrats are protected "insofar as their conduct does not violate clearly established statutory or constitutional rights of which a reasonable person would have known." So if there was a case with publicity, after which that fact changes, then qualified immunity would not apply.
However an obscure case decided in a superior court 30 years ago does not provide sufficient publicity to reverse the fact that reasonable people don't know about the third amendment. So it would in all likelihood apply again.
Incidentally this is not my line of reasoning. I got it from In Our Defense: The Bill of Rights In Action by Caroline Kennedy and Ellen Alderman. Given that they were lawyers writing on a legal topic, I'm inclined to accept their reasoning.
At least in the cases I have read have not assumed publicity. Most of what I have gotten on the subject has been from Orin Kerr's discussion of Ashcroft v. Al-Kidd and a number of other cases (he's a law prof), and some stuff another law prof (Eugene Volokh) has blogged about on some other cases. I make a hobby of actually reading what the courts have said.
Now all this being said, it isn't out of the question for different circuits to have subtly different standards.
As a note dissents on several relatively obscure cases I have read have noted that after the finding of violation that the law will be sufficiently clear for the next case to proceed.
My understanding at least in the circuits I have looked at is that "reasonable person" includes "reasonable person having been advised by a lawyer." Note that a lot of cases really do fall into the case where beforehand reasonable lawyers could disagree as to whether a violation occurred. I think this is what this is usually intended to resolve.
But again there are so many areas of law where circuits adopt remarkably different tests (a hot one right now is airport searches with the 5th and 11th circuits giving the TSA largely a blank check and the the 3rd and 9th circuits saying there are limits but not yet having found that those limits have been exceeded).
I believe that the point made before the courts was that a legal principle that had not shown up once in litigation in nearly two hundred years is obscure enough that even a lawyer could be excused for failing to remember its existence.
At this point that would be a legal principle that has shown up only once in over 200 years, and which created precedent supporting the claim that it is so obscure that even a lawyer could be excused for failing to remember its existence.
Obviously a lawyer whose attention was drawn to the 3rd should draw a correct inference. But there is so much to the law, and lawyers focus so much on precedent from previous cases, that a lawyer can be excused for forgetting about it.
The immunity was because a bureaucrat could not be expected to know about the 3rd amendment. Any future violation would be a decision made by a bureaucrat, the same immunity would apply, and the precedent would say that the state wins.
For all intents at this point, the 3rd amendment is null and void.