In a fit of inspiration, I went to work yesterday with fine-tip acrylic marker, moving very lightly and carefully and only filling in the worst areas of missing paint, aiming for the end result to still retain the appropriate amount of wear for a 32 year old guitar.
Try using an oil-based paint pen. I get mine at Walmart, $3.00 and use it for lots of things. Should work great, permanent, and easy to use on the raised TRC lettering.
I totally agree that constantly trying to negate the effects of age and wear on a vintage Rick is a waste of time and negates its "mojo". However, I would certainly do what the OP is suggesting (with a sharpie) if it's the only part of the instrument showing such wear and the rest of it is pristine. It's all about consistency.