If you want to drop “sur le sujet” you have to also drop en and change by s’y.

I don’t have the actual rule in mind, but the s’ refers to “sur le sujet”.

Elle s’y connaît plus que moi.

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a little trick outside of your question.
In France people use mostly :

Elle s’y connaît mieux(plus) que moi sur le sujet.

and

Elle en sait plus que moi sur le sujet.

It’s just that the other sentences (your first one and the correction of the second one) are not that used because they doesn’t sound really good, but are still correct and heared time to time.