If I understand you correctly, what you want to publish doesn't "go against" the previous work. It's fully consistent with it, but what is being added is what are often called negative results: namely, the discovery that a certain plausible method or established theory cannot be used in a certain manner to solve a certain problem.
In every branch of academia I know of, it is -- unfortunately -- very difficult to publish negative results. In the abstract, most people agree that this is a shame: convincingly arguing that researchers should not go down a certain path is obviously a service to the community. However, in a competitive publication system negative results are somehow not very, um, competitive. So trying to publish these results may not be the best use of your time unless you package them carefully -- very crudely, you will probably need to bundle them with "positive results".
The above is a relatively benign interpretation of your Lead Investigator's comments. It is alas also possible that he is saying that you should not try to publish your negative results because that information will reduce the prestige of your previously published paper. I agree that this sounds ethically dubious, yes, but depending on the field it is not clear that you are ethically required to publish further work explaining the limitations of your previous results. Here I would make a distinct between limitations and errors: errors are things that you should have known better than to include in the original version, and in many fields it is appropriate to print a retraction, erratum or corrigendum when you learn about them. On the other hand, that a publication contains ideas that are not completely definitive and whose future value is the subject of informed speculation....well, that's how research works.
I would say that the ethical issues become more acute depending upon the reaction that your published paper has received. If your paper has been very influential to researchers and is causing them to spend a lot of time exploring what you know to be a blind alley, then formal publication or no, it seems ethical to relate this information to them. If your publication has present nonacademic ramifications -- e.g. if you are in some kind of bio-medical field and your publication has resulted in patient protocols that you know to be suboptimal -- then you should be thinking about how to get the word out ASAP.
Anyway, it sounds like you need to have a conversation with your Lead Investigator about this. Find out what he meant and why.