I recently upgraded from LRTimelapse 3 to 4 and have run into trouble with the new workflow. I was used to manually editing the 2 to 3 star frames in Lightroom to fix jumps in exposure but now it seems that this feature is being handled automatically. Problem is that during two recent sunrise timelapses, I (1) removed ND filters during the shoot and (2) changed the aperture on a manual lens. These two jumps in exposure aren't corrected by LRTimelapse 4. Is there a workflow where I can manually correct these kinds of jumps? thanks!

Yes, in that case just use two adjacent 4* keyframes to fix only those jumps via "Exposure", all other (where Exif Data is present) will be corrected in background.