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Okay, so at one point I was shiny hunting rotom in Pokemon USUM but gave up because it was taking way too long. I decided to hunt froakie but I was wondering something. Will the shiny be on the same egg as if I was still hunting shiny rotom or will putting in different parents make it roll again to see which egg will be shiny for froakie?

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Any eggs that you receive while you have at least one foreign parent in the day-care will have better shiny odds, even if you remove the foreign parent before the egg hatches. The same works vice-versa, where any egg received while you have a non-Masuda pair will not have increased odds, even if you put in a foreign parent before the egg hatches.
If you’re talking about egg-swapping, moving from a Masuda pair to a non-Masuda pair will negatively interfere with your chances. But if they’re both Masuda (or both non-Masuda), then you’ll get a shiny on the same egg if you switch out the parents.

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You know how its predetermined what egg will be shiny? What I'm saying is, will the system re-roll for froakie for the chance of it to be shiny or will it be the same as if rotom was still in the day care? Both of them are Masuda Methods. I am just changing to froakie because I became bored of looking for rotom. I just want to know if the shiny froakie will appear at the same egg shiny rotom was predetermined to appear. I don't know if it re-rolled for froakie.
Ah, yes, it will be the same for both. I’ll edit that into the answer.