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If user comes to my website with utm_source in URL e.g. http://example.com/somepage.html?utm_source=affilate after that user visits several page on same website and comes to checkout page. In between utm_source is not in URL of any page user visit including https at checkout process.

If this user purchases then will that user correct utm_source reflect in Google Analytics?

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In the asychronous code (ga.js) this information is stored in a cookie (__utmz).

In Universal Analytics this info is stored on the Google Servers and retrivied by Google via the user id (which, again, is stored in a cookie, only that Universal Analytics stores nothing but the user id).

Which means that a lot of scripts that rely on information from the Google utmz cookie will fail after the migration from asychronous tracking to Universal Analytics (Google just announced that the upgrade is mandatory and that indeed old accounts will be "auto-transfered" to Universal Analytics).

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Yes. Only the first link needs to have the utm_source and related analytics parameters. As long as the Google Analytics javascript snippet is correctly configured and included on every page of the website (or at least on the first page) this will collect the values and associated them with the user.

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