Why does my app's cookie disappear during the checkout process?

Shopify Partner
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Hello there,

I'm developing an app that relies on a cookie previously set by the same app. In the shop everything is working fine, but as soon as I enter checkout that cookie is gone. I want to retrieve the cookies value after checkout with the Pixel API which seems like it would work, but the cookie is apparently gone/unavailable during the whole checkout process, I can't even see it in the browser console.
I can't find any info about cookies set by an app being deleted by the checkout process and it seems a little odd since the Pixel APIs checkout_completed event explicitly gives the functionality to read cookie values.

So is this intended behavior, am I missing something or is what I'm trying to do just not possible?
Thank you!

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