We often work with N-Boc protected compounds, and the extraction protocols sometimes call for 1 M HCl. Even if the next step were washing with bicarbonate, this makes me uneasy, due to possible loss of the N-Boc group. However, I am uncertain of the best alternative and whether or not the best alternative depends on context. Using 0.1 M HCl or using 5% NaHSO4 or KHSO4 are possible alternatives. I occasionally see citric acid in wash steps, and I imagine its chelating abilities might be useful in certain work-ups. This question has come up before, but I don't recall that it was resolved.