Tell your employer that when they contribute the remaining $750 to your HSA administrator, to tell them that it is a contribution for tax year 2017 (this is important!). They are able to do this up until the due date of your return.

However, it's up until the due date of your return with extensions. If you feel that your employer may not make the April 17 2018 deadline but would make the October 15, 2018 deadline, then file the extension to give you (them) that extra time.

Note that just because you file an extension, this does not mean you can't go ahead and file whenever you're ready.

Your danger is that if you file using your current W-2, that your employer will mess around and never deposit the other $750. That will involve filing an amended return and perhaps paying back some of your refund (if any).

The IRS rep is right, you can file a missing or incorrect W-2. Note that if you do e-file, that the refund process is independent of any amendment process. You'll get your refund - you just might not want to spend it all, pending any amendment that you may or may not have to make.