Is re-taking a course seen negatively in PhD applications?
I doubt that it would be seen negatively by most reviewers, but who can speak for everyone. It shows some evidence of seriousness.
But it might not be necessary, in fact, especially if this is for application to a US institution where the acceptance is based on an overall assessment of the likelihood of success without individual small things having much effect. If you have letters of recommendation predicting your success then it probably isn't necessary to retake the course.
But the &quot;hardest and most useful&quot; comment suggests that it might be worth it.
But if you are ready to make application now and the course would delay that, then there is no reason you can't do both. Send off a few applications and also register for the course.

Caveat: In France things might be different, especially if you have a masters and not just a bachelors. But in the US you would likely have an opportunity to learn the required material as part of early doctoral studies.