You can get fly strike, which can be fatal. BUT a guinea pig that is basically healthy and able to keep its bottom clean shouldn't be at significant risk - as long as there's no injuries they should be able to clean off any eggs before they hatch and so prevent it. You can minimise the risk by keeping their cage/hutch as clean as possible so the flies have as little to draw them near as possible
as long as you are checking through their fur for any irritation from scratching every few days and are keeping an eye on them if there are a ton a flys then it should be fine
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