Your Google Ads campaigns won’t be “broken” because the ads themselves are independent of the platform. However, tracking and conversions may be affected if you don’t properly set up the relevant codes. About the GA4, You’ll need to add your GA4 tracking ID to Shopify. This can be done in Shopify’s Preferences settings by pasting your GA4 Measurement ID.
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To ensure Google Merchant Center continues to function after migrating to Shopify, set up the Shopify Google channel to sync products, verify and claim your new Shopify domain in Merchant Center, update shipping and tax settings to match, confirm that the new product feed is connected to your Google Ads account if running Shopping Ads, and monitor the Diagnostics tab for any product feed errors.
Cloning two website is actually good and nice. But doing it yourself might look somehow.
Am suggesting if you can share me your store link so I can put you through how to about it and also for perfect seo done. But are you sure Cloning and seo is the best thing to be done to your store. You can share me where we can talk better so we discussed better there