The non-conforming or altered box lets IRS know that either original W-2 was not available or you had to "fix" it to enter (like a transposed SSN that will get correction from employer eventially) It works well in efile as long as you have EIN

I am in TX so I do not have to deal with many California W-2.  I glare at clients if they think about moving to states that have income tax!

You could probably get the IRS return to clear efile by telling the program to NOT do error ck as you efile BUT that would give you more grief when you go to the state filing. So you will need to try to get the state # from somewhere (the company payroll dept or another employee or the prior yr return if he was a long term employee--research the options with client) because you know that CA does not want a paper filing.