See clip from Attorney Rajiv S. Khanna's conference call video that addresses this question.
This FAQ is on “filing amendment for pending H-1B petitions”.
Let me explain to you, what the problem is. Let’s say I apply H-1B for myself and I am going to work for IBM as the end client. When we filed the case suddenly in 3 months my client changes now I am going to work with Sun Micro systems. Can I file amendment in midstream and the answer is very problematic.
Normally, USCIS they used to be OK until a year ago. Last year or so USCIS have been saying if your situation changes while the case is pending, we will not accept the change. You have to file H-1 again and if you are out of status you have to go outside USA for visa stamping.
See in your spouse’s case there is little bit of a better situation. In that she is still on H-4 maintaining status. They applied for amendment separately, it might work. If she is a quota case that becomes another problem because if first case is not approved tenth amendment cannot be approved, just keep that in mind.