You can go to the Transit info panel, and select the metro/subway tab. Then scroll through the list of subway lines. When your pointer is over top of a line, it will glow on the (now white) city map (even if it was hidden - we're about to get to "hidden").
Feel free to also change the color of the line so it is distinctive and you know you're not handling another line by mistake.
Once you know which line it is, note the "eye" icon in the leftmost column of the chart. That will make the line visible or invisible. The eye at the top will show or hide ALL the lines.
So hide all the lines, then show only the line you wish to edit/delete.
Having done so, now go to the bottom-edge menu. Select transit and the tab for subway (or whichever) and the route creation tool. Now you are seeing only the line you wish to change, because you hid the others.
Float over the dot at a station. You can drag the line to add stops, drag a node to move stops, or right-click the node to delete the stop.