Generally if I discover there is a significant low at that time I'll skim it it with Ice (flowing polyester filler), get it flat, and then reshoot the 2k over top of it and try again. That is part of the repeat as necessary step. I am a fanatic about dead flat smooth surfaces on the jobs I turn out and so I may find myself redoing it two or three times if necessary. At any rate the epoxy is first and last. I shoot it first over the bare metal to seal it against any chance of later corrosion, then I do my work, then when all is said and done I will shoot two more coats of the same epoxy paint, only thinned slightly this time, as a color sealer. And that is the thing about epoxy, it is that final sealer that locks down everything under it.
As for the earlier question, about finding existing filler under an old paint job. I know guys who say that if it has held out this long leave it alone. My thinking is that I am the one who guarantees my work and I don't feel very comfortable guaranteeing someone else's work. So I grind it out and redo the work in a fashion that I know with certainty is sound. I think that's very important if for no other reason than the cost of the paint that will follow.
Just for reference, now and then I will paint a bike for a friend, and generally I'll just do it for the cost of materials. In general that means they are going to have to lay out something like $200~300 (typical real-fire flame job over a solid base color) just for the paint and tape (all leftovers belong to the painter) depending on how complicated it is. So even in those cheapest of jobs there is still enough money on the line that failure is not an option; and of course there is reputation, something that no painter can afford to lose.
