Shopify and Paypal

We make sales on various platforms including Shopify, at the end of the month I run the sales report for Shopify and enter the details into Quickfile. Separate to that we have transactions going through Paypal as some shoppers pay that way, if I post the Paypal payments and refunds I am duplicating the transaction, however I need to keep the Paypal account feed for transfers. Does anyone else have this issue and if so, how do you deal with it?

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