EDIT: Shopify's support is limited when it comes to third party payments and gateways such as Paypal. As Shopify does not accept the payment, our support can not see why a payment might be pending. If what I've mentioned below does not solve your query, please contact your gateway provider's customer service directly as they'll be able to see the payment in full and provide more info. Paypal's support can be contacted here. If you would like to use a different provider, please check out this guide for a list of alternative gateways you can connect with.
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 emailor 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!
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