I recently upgraded to QB 2019 Desktop from QB 2016 Desktop. Although my preferences are set to warn me about duplicate bill #'s for the same vendor, this feature is not working. We import our payables from another system by .iif files. This feature worked fine with our 2016 version.
Let's try some troubleshooting steps by toggling the Warn about duplicate bill numbers from same vendor feature to warn you on the duplicated bill numbers.
To toggle, you'll just have to uncheck Warn about duplicate bill numbers from same vendor. Then, click save and mark it again. Once done, let's import your payables from another system by .iif files in QuickBooks Desktop.