I have been using LRTimelapse 2 for a few years for deflickering and it works perfectly. I recently upgraded to 4.6 Pro and can't get it to work. After clicking the "deflicker" button, I can see the plus and minus values in a new column but clicking "save" doesn't apply the adjustment to the exposure. All images in the sequence still have exposure of zero. Any idea how I can get it to work? Thank you!

Deflicker will not get applied to "Exposur" anymore. It will be applied in background, as it will happen for the HG adjustments. This makes things much easier, since you can still edit Exposure as you like without losing the other adjustments. Please watch my new tutorials since the workflow has changed in LRT4 compared to LRT2. http://lrtimelapse.com/tutorial

This is a really good new feature, and the visual workflow is fantastic too!

I notice that we can now add a graduated filter in keyframes and lrtimelapse will add the auto transitions for the change of its position and value. Should I keep the filter in every keyframe, even in those frames that I don't want to apply the filter? Or I should keep it and manually adjust the value to zero?

You must not remove the filters, just leave or set the values to zero where you don't need them.