If you're having trouble tracking customers as they navigate your site, and move onto checkout, this is likely because a cookie is being reset. One of the most common reasons we've seen a cookie get reset is having the top-level domain (TLD) change.
A Quick Primer on TLDs
The TLD is your website's main domain name. For example: google.com is a TLD. However, there may also subdomains such as news.google.com. In this case google.com is still the TLD.
TLD and Cookies
When using cookies to track customers it is required that the TLD remain the same. For example, if a user visits your site hosted at my-store.com, in order to properly track them they also have to checkout on the same TLD (my-store.com).
Similar to the example above, your TLD can have a subdomain. Most commonly this will look something like: checkout.my-store.com. Notice that the TLD remains the same (my-store.com). Having the same TLD will ensure that cookies remain the same, and as a result tracking occurs as intended.
However, if at some point your TLD changes, this will cause the customer's browser to create a new cookie, and will break the tracking process. For example, a user enters your site through my-store.com, but checkouts on my-store.shopify.com, by moving from my-store.com to shopify.com, the browser will issue a new cookie to the user.
To ensure that you are accurately tracking users as they navigate and checkout on your site, it is important to make sure they stay on the same TLD, so as to not break the tracking process.