How many years one speaks a native language is not relevant to this discussion. One's claim is not further supported by such information.
If you think that "I thought I had replied" is more correct than "I thought I replied", then you should have a reason. In my view, a reason, such as yours, would be based on such things as this: formal is more correct; perceived notions of "classroom English"; the grammar books seem to indicate that it is more correct. Just the same, grammar books present the past perfect, it still does not correct that sentences must follow this model or pattern: I thought I had replied. Using the simple past in the second clause is equally correct: I thought I replied.
I meant to communicate that when completely divorced from context, there is now nothing we can say about their correctness; that correctness has a good deal to do with context.
For example "the right" vs "the right-hand side." Both sound like normal English. But if we have a specific context, one may fit much better, to the point that the other is not as good, such as in politics.
Even in such contexts which may exist, it is not necessarily the best thing to do to force the use of the past perfect in places where it is not absolutely necessary to form a correct sentence, speaking in terms of how one teaches that is - and otherwise I suppose. So the issue really seems to be that you think the past perfect is necessary in certain situations, and I say in certain situations the past perfect is possible, but it is not absolutely necessary in all such contexts to form a correct and intelligible sentence. If you agree that this is where our paths split, then I'm prepared to say "let's agree to disagree".
Well if you give a symmetrical account, I'll agree to disagree. But if you write "absolutely in all contexts" I'm hesitant. I would say that in certain contexts, the pluperfect is required. In others, it's not necessary. So I agree with you about some of it.