Will an eCheque refund change if funds added to account?

[OutdoorsGroup]

We've been refunding customers but hadn't realised our account balance was at £0.00 so it has been issuing them as eCheques. We've now transferred funds from our bank account to our PayPal account but this is still processing. Once the funds are in our PayPal account, will the refunds automatically be deducted from our balance or will they remain as eCheques? Is there any way to ensure the refunds come from our balance retrospectively?

Thanks in advance for your help!

[kernowlass]

@OutdoorsGroup 

You can't change a processing payment or refund once made, so all the refund that you have already done will come from your bank account.