The modification is a proper part of the design of the product. So, no, don't "hand draw that on the PDF".
Add it to the schematics. You should have proper versioning control for your schematics anyway (Try git. It's thought for source code, but it works with any file type – you just won't get useful differences displayed between revisions, but that's not a problem here). Clearly annotate it in your schematics. If your EDA suite allows that, change color, stroke, whatever of the modification to make clear it's a modification.
If your modification is just a wire bridge: it's not uncommon for schematic design programs to have some kind of special "external connection" component.
Since you're probably want to still be able to generate a valid board from that schematic, make sure the "external connection" component you have has a small single pad that you can place on a wire in your board design. That way, you also get a guarantee you have something to solder too in the end.
Again, I don't know what software you use, but it will still make sense to "formalize" even the crudest hack into some kind of footprint/component: your wire bridge could simply consist of two components with one pad each, which share the same net name. That way, you could actually "place" the fix in your board design, and hence, have it documented.
Also, your board might fail design rule checks. Which would obviously be correct.