Does anyone know if this pop up on a sales order is a feature that needs to be disabled or a script? "Items on this line have been drop shipped or special ordered. Are you sure you want to modify it?"

I've seen something similar when you try to modify a line in a sales order that has been fulfilled. Or an invoice that has been paid already. It's NetSuite's default behavior.

It appears to be a message when you are trying to change a line item when there is already a PO.

It's just NetSuite's courtesy warning because the line already has a dropship or special order PO related to it. If you change, say quantity, or location, the PO won't automatically make the change accordingly, and you have to manually update the related PO if needed. So the warning is more of warning about potential SO/PO mismatch, and/or potential action item for you to manually update the related PO accordingly