Can you give us more information about the entries that you are trying to clear? so that we can provide the best resolution.
If these deposits we're matched and made directly from the bank feeds. You'll need to unlink it first before you can delete it.
Here's how:
1. Go to the Banking or Transaction menu and select the bank account.
2. From the Reviewed or Categorized tab, locate the deposit transaction.
3. Click on Undo.
Then, you can reach out to your accountant before deleting the deposit transaction. Also, you can exclude the downloaded transaction if you don't want it to show on your Banking. From the For Review tab, locate and checkmark the transaction, then click Exclude.