In my defence: I am not aux fais with autoharp string availability,
but surely there are brass wound and copper wound strings out there, by choosing different ones for certain notes (black notes?) it would help. It would mean changing some strings and tuning them.

A sharpie would be a good alternative, on wound strings because the colour would only rub off on the ridges and there would still be some colour visible. Lessening as you gain experience and need the colour less.

As for changing the pitch - if you have perfect pitch you don't need the Sharpies. And for the minor change in frequency - you can re-tune.

non-wound strings you would have to mark the posts and the button bridge as well - and get used to parallax. Some colour would remain but not be that useful.

Sorry to harp on - I am in auto.................