It's been a good many years since I've looked closely at that kit, so any suggestions I offer have to rely on my highly defective memory. That said, the best I can suggest is to fill the sink marks with a high-quality epoxy putty, like Miliput. It shrinks considerably less than the garden-variety stuff, and leaves a relatively smooth surface; if you're careful you may be able, with some practice (of which you'll get plenty in the course of fixing all these portlids), to do the trick with an application of putty and a coat of paint. (You want, if possible, to avoid sanding or filing, which will risk damaging the hinge detail.)
About the only other idea I can think of offhand requires casting equipment (which, given the small size of the parts in question, actually doesn't need to be such a big deal). You could fix one of the portlids and use it as a master to cast replacements for all the others.
Maybe somebody else can come up with a better idea; those are the only ones I can think of. Good luck.
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