If you have 2 lots of the transfer, so that the original is duplicated, you should be able to safely delete the untagged entry. Providing your balances are correct, you should be good to go 
I think what may have happened here is the PayPal feed is picking up on deposits on your account which is causing the duplicates. If you go to your PayPal bank account within QuickFile, you should be able to select More Options >> Feed Settings:
On this screen, you will see an option for transfers:
If you tick this box, any transfers that we receive from PayPal, we will simply ignore, so you can input them yourself manually.
I hope that helps?