I face this often .. and would love to get a list of all the controls that do not 'work' for LRT .. Gunther has been amazing to answer all my mails so far .. from what I am able to gather from above thread and other info - if your changes in Lightroom are too strong, LRT " doesn't like it " and behaves in a way to equalize the entire sequence to an average / flat look .. defeating the whole purpose of the shoot ..
No, it's just that if you use controls in the Basic Panel, Lightroom will apply them in a context sensitive way. That means, different brightnesses in the source images will lead to contrast changes after editing.
If your source sequence is rather clean and steady (shot with an ND filter, no harsh contrast changes etc.), you won't have any issues, even with those tools. But if you have big differences between source images (car lamps coming in, people passing by quickly etc.) you might notice that Lightroom introduces contrast flicker.
In such cases, use the tonecurve controls to control contrast, instead of Blacks/Whites/Shadows/Highlights/Dehaze/Clarity in the Basic panel.