I understand that you need to turn off the warnings. Let me share details about it.
Usually, the purpose of the pop-ups and warnings in QuickBooks Online is to make sure you're making the right changes. Since you're trying to edit the downloaded transactions with matched entries, it's normal for QuickBooks Online to behave this way especially if they are reconciled. Currently, we're unable to disable them.
The warnings we can turn off are those related to transaction numbers. Go to the Gear icon and select Account and settings. From the Advanced tab, review the Other preferences section.
I've added some you might be interested in. These will discuss more on how to manage your transactions in QuickBooks Online.