I doubt they were in production around the time FR/LG were released, unless we're talking about very early prototype versions. However, I think creating a new generation was on GameFreak's minds at the time. The Kanto games had to sit through another two generations before they were remade, and it's likely that they thought remakes of the Johto generation would have been too soon if they were featured in the third gen period (especially when you consider the probability that the Kanto part of the games would have been almost identical to FR/LG, but exploring the region in a different order).
I'm going to say that they began production after D/P. Remakes were probably considered earlier on, but it's unlikely production was.
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