For your task, instead of a direct translation, try adding a "distillation" step in between. Have it take the raw format and distill the important parts to yaml or whatever, then take the distillation and translate that into the new format. That way you can muck with the yaml by hand before translating it back, which should make it easier to keep the intent without the spaghetti getting in the way. Then you can hand-wire any "complexities" into the resulting new code by hand, avoiding the slop it would more likely create.

It may even be worth having it write a parser/evaluator that does these steps in a deterministic fashion. Probably won't work, but maybe worth a shot. So long as it does each translation as a separate step, maybe at least one of them will end up working well enough, and that'll be a huge time saver for that particular task.