There is no issue with the flow, it appears to be an integration issue and change with the new theme, in conjunction with Shopify having a new Add to Cart tracking pixel (apparently)
Apparently (from chat) Klaviyo now recommends migrating Shopify stores to the new shopify-branded Added To Cart event which is tracking through Shopify pixel rather than the old code snippet.
Hey
The old Added to Cart snippet and the newer Shopify-branded Added to Cart event (synced via Shopify's server pixel) are two separate metrics in Klaviyo, and theme updates commonly break the old snippet since it depends on your theme's JavaScript loading it correctly. The Shopify pixel version doesn't have that dependency, which is why Klaviyo has been steering accounts toward it.
Check your Metrics list. If you see two separate Added to Cart entries, one with a gear icon and one with a Shopify icon, you're running both in parallel and the gear-icon one is what broke. The fix isn't patching the old snippet, it's updating your flow triggers and any segments referencing the old event to point at the Shopify-branded one instead, then removing the old snippet once everything's confirmed working. Klaviyo has a full migration guide for this exact swap if you want the step by step. Article here
I hope this helps and thank you for sharing your question here in the community.
Cheers
Arpit
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