Does that mean that failure to take down an article is criminal if posting that article would now be criminal?

No idea, but the period of prescription starts when a libelous/harassing item is taken down.

I learned this because of a recent scandal where numerous, well connected, French journalists were operating coordinated 4chan-like online raids and IRL harassment on colleagues they didn't like.

https://fr.wikipedia.org/wiki/Ligue_du_LOL — Literally the "League of LOL"

I guess so, and the fine would be proportional to how long it has been illegal.

It is a continuous crime. Ressa and her company were requested to take down the libelous article but they didn't heed it.