Well, Flootenkerp is stating a fact, i.e., its not slander if its true. As much as you think your sources are reliable, not all of them are.
I know you probably don't go to your debate forum much. But if you were to put this up there, your argument is full of fallacies.
Whether your new information is reliable has nothing to do with whether your site is popular. Maybe you had only reliable sources at some point and that made it get popular. You will continue to be popular until another site comes with more reliable information and more reliable sources and people start noticing that. By the time DP came out your site was already popular. People take what you say on faith. I would like to point at this post from pojo: http://www.pojo.biz/board/showpost.php?p=11640160&postcount=5
People assume you have reliable information from reliable sources and by putting blatantly false information you are doing a disservice to the community. Its much better to say "At this time we don't know how _____ works".
Also the fix you made does not do jutice to the complexity of honey tree pokemon, but at least it does not have false information now, which is the important thing. Better to have too little information, instead of alot of false information.
Now, you should take what Flootenkerp is saying as a wake up call. Not as some sort of insult. He did not say it in an insulting manner (I have seen many statements by him and trust me he put this very nicely). If someone says that not all your sources are reliable, then you have to think about who are your sources and figure out how to address the issue, so it does not continue happening. Of course, you have to ask yourself, who is saying that as well and what is their reason. But when you have a reliable source and people from his site saying that you have some unreliable sources, you should take a hint. (I consider myself a reliable source to Serebii.net )
Don't just take it on faith that your sources are reliable. Although I can see where that can get hard to do, because there is some information which you would have a very hard time verifying. In particular verifying the munchlax honey tree mechanics can be a bit difficult for someone who does not have the technical skill that me an Sabresite have. But as the owner of a site that claims to have correct information its up to you to address the issue. It can be as simple as not taking any more information from the person who told you that it was 1% at each tree. Or maybe your solution can be more complicated I don't know.