I have not encountered this before and thought it might be related to the retirement of flash player for web, though I thought this did not affect the swf format outside of a web browser, only the flash player itself. I exported the swf from Toonboom Harmony (v14) and the lines appear to be jagged on some of the shapes instead of smooth.
You'd be better off asking in the Animate or After Effects forums, but my suspicion is that it has to do with the quality of the export. While Flash does support bitmaps, Flash objects are generally defined as vectors, and Flash Player is definitely capable of drawing high quality, anti-aliased vector graphics. That said, we're going to render whatever got defined in the SWF. My guess is that the export tool in the software you're using (I've never heard of it before) is the source of the output issue.
I'm pretty sure that Animate and After Effects use specialized Flash binaries that are built into those respective products, so they shouldn't be dependent on the generally available Flash Player browser plug-in(s) on your system.
If you have a specific question about Animate or After Effects, you're probably better off asking in those respective forums, but my sense is that this is an issue with the quality of the source document.
Thank you for the reply. So it definitely could be a Toonboom issue. One thing to clarify is that the image I posted is showing up a bit pixellated, but it is just a screenshot of a closeup of vector art. The final image was vector and scalable without pixilation issues. Instead, when I say jagged I'm referring to that the lines are made of fewer vector points so that they appear like a series of straight lines instead of smooth like a bezier curve.
I spend a lot of time in Illustrator with Live Trace, and this struck me as one those instances where you don't have the digitization settings right and you're getting an appoximation of a drawn curve (made out of a bunch of little segments) instead of a single bezier curve.
I'm assuming that you started out with original art that had actual bezier curves and not a bunch of segments approximating a curve. It sure looks like the final output is a bunch of segments approximating a curve, and from my understanding of your workflow, the only thing between that original source and final output is Toonboom.