There are pens designed for marking on
CDs. I would try these.

There may also be alternative plastic sheeting
(mylar perhaps?)  which may be more suitable for
marking.

I have an interest in restoration of faded cels as
it is a topic that nobody seems to have covered.

There seem to be other factors which contribute to
fading of copier lines -- not all of it due to UV.
There seems to be a chemical reaction, perhaps
from some paints, perhaps a combination of
factors, which degrades the toner. AFAIK nobody
has investigated this further.

Most fans seem to consider faded cels worthless,
although I think with a little work one could
easily restore them.

-Dan
(To reply in email replace blort dot invalid with
anime dot net)