I just did that on mine using a china black pencil (grease pencil). Looks great, doesn't stain the wrist, trivial to remove if you want to---it actually wears off by itself in a few weeks.
If you fill it with a black enamel pen, it will look great. Since it was black paint anyway, why not?
Typically its India Ink that is used to fill in the letters/numbers on bezels or casebacks, it's thin and durable. Put down a coat of ink, let it dry (don't worry about getting it perfect in the engraving, you clean off any excess when you are done) then put down another coat, let it dry fully, then with a sharpened toothpick clean off any excess ink on the caseback and you are back to the original condition. Replacing the missing ink should have no effect on collectors value of the piece, if it does, simply scrape out the ink and its back to where it was.
Threads on the Omega Forum in 20 years: "The lume looks refinished, and that doesn't look like factory ink on the back."
I wish I had a nickle for every time I've asked myself this same question. My 1973 Speedy lost it's black lettering sometime in the distant past. I've resisted doing anything about it for decades out of laziness/fear of "modifying" it. I appreciate the inputs.