I already emailed this to Phil, but I'll repeat here for the benefit of the group... I know an iPad Pro + Apple Pencil user who has used this workflow:
From 1Chart, he exports a PDF into ForScore and marks it up with an annotation layer. If he then edits the original chart in 1Chart, he can re-export it into ForScore, where it overwrites the old PDF — but maintains the ForScore annotation layer.
Just to be clear, there's no re-importing of the original PDF back into 1Chart in this scenario, or any other scenario. 1Chart can't import PDFs. It can only import 1Chart files or 1Chart notebooks.
If you are viewing in iBooks, there’s markup right in there (works nicely with Pencil). Otherwise any annotation PDF app should work, most seem to support the Pencil now and I see several of the ones I have list when I share the 1Chart.
It depends on what app you use for viewing (or if you print it out on paper).
You could always make a screenshot and draw on that before saving it to Photos. In iOS11 the screenshot momentarily shows as a thumbnail bottom left and if you tap it before it disappears, you can do markups with (finger or) Pencil before saving to Photos. You can crop out the top menu if desired although it will change its proportion.
Using the Pencil is a very nice experience. I have a cover with a pencil holder (STM). I find it useful to turn off Bluetooth when not needed, otherwise the pencil battery can drain quickly.