Did Jello stop making lemon cook and serve not instant pudding?

It seems you might be a little mixed up! Jell-O doesn't make "cook and serve" pudding, that's a product made by Kraft. Jell-O is known for their gelatin desserts.

However, Kraft does make a lemon pudding mix, both in an instant and cook and serve variety.

So, to answer your question directly, Jell-O doesn't make lemon pudding, so they haven't stopped making it. Kraft, on the other hand, still makes both instant and cook and serve lemon pudding mixes.