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Do you have a litter tray for her?
If not find a small dish & fill it with chinchilla sand, not dust, put some soiled substrate on top & place it near the nest, she should begin to use that. How long have you had her? Peeing in the nest with new ones isn't that uncommon if they're a bit nervous about coming out.
Is she nesting in a house or open nest?
With plastic houses the condensation & ammonia build up really isn't healthy, wooden houses are better but they do need a coat of plastikote to water proof them, once they've peed on untreated wood you never get the smell out so they tend to keep on doing it.
I would try not to remove too much of the nest, just take out anything wet daily & leave the rest while she continues to do it, with any luck she'll start using the litter tray if she has one.