The control number in box d is not required by the IRS - it is used by your employer.As a result, if it causing you trouble, just delete it.If it is not causing you trouble, then leave it in - it won't matter.
If you get errors when attempting to e-file with an empty box D, just enter any number in this format: 5 digits, space, 5 digits (for example 12345 67890). The IRS doesn't care what's in box D.