They are interchangeable. The difference between them is only a stylistic one. In writing, I would use the first sentence if it came right after the event where you saw her for the first time.
I saw a girl at a coffee shop and I thought she was beautiful. And a couple of weeks later, I saw her drinking at a bar.
But if there were more sentences in between, I would use your second sentence to make it clear that I was referring back to the event at the coffee shop.
I saw a girl at a coffee shop and I thought she was beautiful. I was drinking a double espresso because I was very tired from the night before, and I had to leave for a business trip that morning. So it was quite some time before I thought about the girl again. But a couple of weeks after I'd seen her on that day, I saw her drinking at a bar.
Something like that. The specificity of "after I'd seen her on that day" gives you the ability to refer back to an event you've already moved away from. Otherwise it's not really necessary and "later" is much more concise.