Oh huh, I'm using an Edding 140S, in case it matters. It was what they gave me when I asked for a permanent marker, and it worked beautifully. Didn't dissolve at all in the etchant, yet wipes right off with some alcohol.
As long as it works or can be fixed with some bodge, I'm okay with that for prototypes. I do tend to tin the traces wherever they seem 'porous'. For broken traces, I use wrapping wire core soldered on tracks.