Gunther, I may have badly explain myself.

LRtimelapse produced the brightness issue that you saw, and it didn't show up in preview. So what I did is do all the LRtimelapse process, then export from LR, then check in folder which pictures were concerned, retouch them in LR to make them match other pictures around it, then create the timelapse. It worked that way

If that helps you find where LRtimelapse bugs, each time it was a picture tagged with 3 stars with the previous one tagged with 2 stars (I didn't do the tagging).

I was also wondering, is there a difference in the video quality between RAW with AE and LRtimelapse for everything ?

I'm pretty confident this is not a bug, since it's one of the core features in LRT that thousands of users are using. It's something wrong with your workflow. I can only say that I expect it not to happen, if you give it a clean start via Metadata/Initialize and go though the workflow as it's intended and described here: https://lrtimelapse.com/workflow/