There is generally no nuance in the form chosen. In usage, they mean the same. Any nuance will come with the context and the way the sentences are spoken.
I recommend that you not take this pill.
I recommend that you not take this pill. [But I can't stop you]
Similarly for the other form.
To be honest, they both sound OK to me. But the form with the auxiliary "do" is probably more grammatical.
"I recommend that you not do something."
"I recommend that you do not do something."
We say: "Take this pill" and "Don't take this pill", not "Not take this pill."
"I recommend that you take ..."
"I recommend that you don't take ..."