You can just leave that field blank and you can still e-file.
The IRS doesn't care what's in Box D because its use by payroll departments is optional.
A Control Number (Box D) is used by many companies to uniquely identify a 1099 in their system. If your 1099 doesn't have one, it's no big deal – you can simply leave it blank.
Now, if you're trying to import your 1099 and you're persistently being asked to enter something in Box D, click skip import to get past this screen and manually enter your 1099 (which should only take a few minutes anyway).