Ted here from Shopify, thanks for reaching out to us!
Since this post was written, has Paypal adjusted the payment status in the account? When an order is paid through Paypal, the funds should be immediately available unless the customer paid with an "eCheck" which can take up to 7 business days to clear. If this were the case though, it would show a pending payment status on the order within your Shopify admin.
If that doesn't help locate your funds, I'd recommend logging back into your Shopify admin and then clicking Settings > Payment Providers > Paypal to see which Paypal account/email is attached to your store. If this is a new account, then Paypal would have sent you an email so that you can get the proper account type setup to accept the funds.
If you did not receive that email or if the email listed in Settings > Payment Providers section is different from the account you're using, then you will need to check the history of the order in your Shopify admin. If you click on the order, scroll down to the order timeline then click on the payment line, this will expand a variety of information, however, you will need to locate the Auth number, Token number and email if it's listed. With this information in hand, you can then contact Paypal's Support here who will help locate the funds.
Please let me know how this goes!
I am having a similar issue. I have the same email address for PayPal that I do for Shopify.
Paypal is holding some of my payments, but not all of them. In Paypal it says the payments are on hold. When I click for more details it wants me to provide a tracking number for the order or have the customer confirm the order.
Most of my orders are in town deliveries done by me, so there is no tracking info. Also, most people aren't going to confirm their order because that is not typically asked. I think my customers might think it is spam and delete the email.
I have reached out to Paypal and they said I will get my payment within 21 days. This cannot be! How can they hold the payment for that long??
Does this happen to everyone? If so, how do people operate their business like this?
I feel like my hands are tied because Shopify requires a paypal account and everyone has paypal.
Any suggestions or help would be greatly appreciated.