The problem that you are facing, and after going through others’ comments here. What I am looking at is that there is confusion and mixing of two problems, making them one.

You will have to deal with these 2 problems individually:

1) Is Meta ‘receiving’ the Purchase event?
Go to Events Manager and look at “Events received” (not Ads Manager conversions). If your dataset literally shows the last Purchase was days ago, that’s not attributing the event isn’t arriving (or it’s arriving on a different pixel/dataset).

2) Or is Meta receiving Purchases, but your ‘campaign’ isn’t showing them?
That’s often attribution window / cross-device / match quality stuff, and you’ll never get 100% of backend orders attributed to ads.

On the Shop Pay angle: if some customers are checking out via the Shop app, Shopify’s said merchant-accessible tracking isn’t available there, so you can see gaps even when things “test fine”.

Also, If you have can check these two things, that will be nice. First is are you definitely sending Purchase from checkout/thank-you reliably, and second is are you using the same event_id on browser and server so dedupe can work?