From 1936 to 1948 the AT went through Harpers Ferry, but hikers had to be polled across the Shenandoah in flat bottom punts.
For a while those choosing to go through HF had to walk over the Potomac on a RR bridge.
In 1948 the Trail was rerouted across Sandy Hook bridge. That's changed.
Now you just follow the usual white blazes over the rivers and thru town.