PDFs were not made to be editable other than those produced by Adobe Illustrator which deliberately embed enough information to enable lossless editing.
The PDFs you find floating around are almost always “finalized” by subsetting fonts, flattening shapes, clipping invisible parts of objects, and/or encryption.
That said, when I was editing the MTA map many years ago, the greatest difficulty I ran into was finding substitute fonts for the text and letter bullets. The lines themselves are fairly easy to manipulate but cutting, changing colors, and/or creating parallel lines (i.e., to add your own fantasy route running with an existing differently colored route).